PDB Short entry for 5LGN HEADER OXIDOREDUCTASE 07-JUL-16 5LGN TITLE THIENO[3,2-B]PYRROLE-5-CARBOXAMIDES AS NOVEL REVERSIBLE INHIBITORS OF TITLE 2 HISTONE LYSINE DEMETHYLASE KDM1A/LSD1: COMPOUND 19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE COMPND 5 OXIDASE DOMAIN-CONTAINING PROTEIN 2; COMPND 6 EC: 1.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: THE FAD COFACTOR IS INTEGRAL PART OF THE PROTEIN COMPND 9 CHAIN; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: REST COREPRESSOR 1; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: PROTEIN COREST; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RCOR1, KIAA0071, RCOR; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MATTEVI,G.CIOSSANI REVDAT 3 10-JAN-24 5LGN 1 REMARK REVDAT 2 22-MAR-17 5LGN 1 JRNL REVDAT 1 22-FEB-17 5LGN 0 JRNL AUTH L.SARTORI,C.MERCURIO,F.AMIGONI,A.CAPPA,G.FAGA,R.FATTORI, JRNL AUTH 2 E.LEGNAGHI,G.CIOSSANI,A.MATTEVI,G.MERONI,L.MORETTI, JRNL AUTH 3 V.CECATIELLO,S.PASQUALATO,A.ROMUSSI,F.THALER,P.TRIFIRO, JRNL AUTH 4 M.VILLA,S.VULTAGGIO,O.A.BOTRUGNO,P.DESSANTI,S.MINUCCI, JRNL AUTH 5 E.ZAGARRI,D.CARETTONI,L.IUZZOLINO,M.VARASI,P.VIANELLO JRNL TITL THIENO[3,2-B]PYRROLE-5-CARBOXAMIDES AS NEW REVERSIBLE JRNL TITL 2 INHIBITORS OF HISTONE LYSINE DEMETHYLASE KDM1A/LSD1. PART 1: JRNL TITL 3 HIGH-THROUGHPUT SCREENING AND PRELIMINARY EXPLORATION. JRNL REF J. MED. CHEM. V. 60 1673 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28186755 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01018 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 40986 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT : 811 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3930 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6325 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.22000 REMARK 3 B22 (A**2) : -3.08000 REMARK 3 B33 (A**2) : -5.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.405 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.282 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.300 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6535 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6319 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8867 ; 1.341 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14530 ; 0.768 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 801 ; 6.423 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;36.677 ;24.512 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1137 ;18.815 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.862 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 989 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7374 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1482 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3210 ; 6.647 ;11.014 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3209 ; 6.646 ;11.014 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4009 ;10.419 ;16.517 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4010 ;10.418 ;16.518 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3325 ; 6.723 ;11.840 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3326 ; 6.722 ;11.840 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4859 ;11.140 ;17.416 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7664 ;14.921 ;88.763 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7665 ;14.921 ;88.765 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42318 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.99300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4BAY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM TARTRATE 1.2 M AS PRECIPITANT REMARK 280 IN SODIUM CITRATE BUFFER PH 5.6, VAPOR DIFFUSION, TEMPERATURE REMARK 280 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 60.25500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.22000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.71000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.25500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.22000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.71000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.25500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.22000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.71000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.25500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.22000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.71000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLY A 804 OG1 THR A 807 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 630 C - N - CA ANGL. DEV. = 10.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 274 115.90 -37.07 REMARK 500 SER A 286 46.61 -98.74 REMARK 500 MET A 332 -16.30 -145.10 REMARK 500 GLU A 352 102.56 -56.47 REMARK 500 ALA A 365 -175.54 -62.95 REMARK 500 ASN A 366 31.26 -159.93 REMARK 500 GLN A 368 -26.65 125.49 REMARK 500 GLU A 391 -39.19 -34.53 REMARK 500 ASN A 407 -11.89 71.32 REMARK 500 ASP A 429 -33.53 -37.69 REMARK 500 LYS A 496 -70.93 -62.24 REMARK 500 ASN A 518 72.44 -107.04 REMARK 500 SER A 526 -173.86 -69.77 REMARK 500 CYS A 577 -38.48 -37.61 REMARK 500 SER A 687 -76.48 -74.96 REMARK 500 LEU A 701 -79.01 -148.47 REMARK 500 ALA A 761 -44.49 -141.21 REMARK 500 SER A 764 -66.63 -91.41 REMARK 500 TYR A 811 30.80 -141.70 REMARK 500 PRO A 812 173.39 -58.30 REMARK 500 ALA A 813 52.83 31.82 REMARK 500 PRO B 311 154.45 -41.50 REMARK 500 LEU B 316 87.17 -163.16 REMARK 500 ALA B 326 -54.76 -18.85 REMARK 500 THR B 329 29.70 -141.37 REMARK 500 ALA B 330 2.45 -67.07 REMARK 500 PRO B 373 164.17 -49.54 REMARK 500 ASP B 401 54.10 -64.70 REMARK 500 PHE B 402 -37.24 -32.58 REMARK 500 ASN B 411 44.76 -105.22 REMARK 500 ARG B 425 -45.06 -21.23 REMARK 500 ASN B 429 50.76 36.55 REMARK 500 ALA B 439 26.93 -68.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6W0 A 902 DBREF 5LGN A 172 840 UNP O60341 KDM1A_HUMAN 192 860 DBREF 5LGN B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440 SEQADV 5LGN PRO A 171 UNP O60341 EXPRESSION TAG SEQADV 5LGN ASP A 371 UNP O60341 THR 391 CONFLICT SEQRES 1 A 670 PRO SER GLY VAL GLU GLY ALA ALA PHE GLN SER ARG LEU SEQRES 2 A 670 PRO HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE SEQRES 3 A 670 PRO ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL SEQRES 4 A 670 PHE LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU SEQRES 5 A 670 ASP ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU SEQRES 6 A 670 GLN GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU SEQRES 7 A 670 VAL HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU SEQRES 8 A 670 ILE ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO SEQRES 9 A 670 THR LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SER GLY SEQRES 10 A 670 VAL SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SER PHE SEQRES 11 A 670 GLY MET ASP VAL THR LEU LEU GLU ALA ARG ASP ARG VAL SEQRES 12 A 670 GLY GLY ARG VAL ALA THR PHE ARG LYS GLY ASN TYR VAL SEQRES 13 A 670 ALA ASP LEU GLY ALA MET VAL VAL THR GLY LEU GLY GLY SEQRES 14 A 670 ASN PRO MET ALA VAL VAL SER LYS GLN VAL ASN MET GLU SEQRES 15 A 670 LEU ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA SEQRES 16 A 670 ASN GLY GLN ALA ASP ASP VAL LYS VAL PRO LYS GLU LYS SEQRES 17 A 670 ASP GLU MET VAL GLU GLN GLU PHE ASN ARG LEU LEU GLU SEQRES 18 A 670 ALA THR SER TYR LEU SER HIS GLN LEU ASP PHE ASN VAL SEQRES 19 A 670 LEU ASN ASN LYS PRO VAL SER LEU GLY GLN ALA LEU GLU SEQRES 20 A 670 VAL VAL ILE GLN LEU GLN GLU LYS HIS VAL LYS ASP GLU SEQRES 21 A 670 GLN ILE GLU HIS TRP LYS LYS ILE VAL LYS THR GLN GLU SEQRES 22 A 670 GLU LEU LYS GLU LEU LEU ASN LYS MET VAL ASN LEU LYS SEQRES 23 A 670 GLU LYS ILE LYS GLU LEU HIS GLN GLN TYR LYS GLU ALA SEQRES 24 A 670 SER GLU VAL LYS PRO PRO ARG ASP ILE THR ALA GLU PHE SEQRES 25 A 670 LEU VAL LYS SER LYS HIS ARG ASP LEU THR ALA LEU CYS SEQRES 26 A 670 LYS GLU TYR ASP GLU LEU ALA GLU THR GLN GLY LYS LEU SEQRES 27 A 670 GLU GLU LYS LEU GLN GLU LEU GLU ALA ASN PRO PRO SER SEQRES 28 A 670 ASP VAL TYR LEU SER SER ARG ASP ARG GLN ILE LEU ASP SEQRES 29 A 670 TRP HIS PHE ALA ASN LEU GLU PHE ALA ASN ALA THR PRO SEQRES 30 A 670 LEU SER THR LEU SER LEU LYS HIS TRP ASP GLN ASP ASP SEQRES 31 A 670 ASP PHE GLU PHE THR GLY SER HIS LEU THR VAL ARG ASN SEQRES 32 A 670 GLY TYR SER CYS VAL PRO VAL ALA LEU ALA GLU GLY LEU SEQRES 33 A 670 ASP ILE LYS LEU ASN THR ALA VAL ARG GLN VAL ARG TYR SEQRES 34 A 670 THR ALA SER GLY CYS GLU VAL ILE ALA VAL ASN THR ARG SEQRES 35 A 670 SER THR SER GLN THR PHE ILE TYR LYS CYS ASP ALA VAL SEQRES 36 A 670 LEU CYS THR LEU PRO LEU GLY VAL LEU LYS GLN GLN PRO SEQRES 37 A 670 PRO ALA VAL GLN PHE VAL PRO PRO LEU PRO GLU TRP LYS SEQRES 38 A 670 THR SER ALA VAL GLN ARG MET GLY PHE GLY ASN LEU ASN SEQRES 39 A 670 LYS VAL VAL LEU CYS PHE ASP ARG VAL PHE TRP ASP PRO SEQRES 40 A 670 SER VAL ASN LEU PHE GLY HIS VAL GLY SER THR THR ALA SEQRES 41 A 670 SER ARG GLY GLU LEU PHE LEU PHE TRP ASN LEU TYR LYS SEQRES 42 A 670 ALA PRO ILE LEU LEU ALA LEU VAL ALA GLY GLU ALA ALA SEQRES 43 A 670 GLY ILE MET GLU ASN ILE SER ASP ASP VAL ILE VAL GLY SEQRES 44 A 670 ARG CYS LEU ALA ILE LEU LYS GLY ILE PHE GLY SER SER SEQRES 45 A 670 ALA VAL PRO GLN PRO LYS GLU THR VAL VAL SER ARG TRP SEQRES 46 A 670 ARG ALA ASP PRO TRP ALA ARG GLY SER TYR SER TYR VAL SEQRES 47 A 670 ALA ALA GLY SER SER GLY ASN ASP TYR ASP LEU MET ALA SEQRES 48 A 670 GLN PRO ILE THR PRO GLY PRO SER ILE PRO GLY ALA PRO SEQRES 49 A 670 GLN PRO ILE PRO ARG LEU PHE PHE ALA GLY GLU HIS THR SEQRES 50 A 670 ILE ARG ASN TYR PRO ALA THR VAL HIS GLY ALA LEU LEU SEQRES 51 A 670 SER GLY LEU ARG GLU ALA GLY ARG ILE ALA ASP GLN PHE SEQRES 52 A 670 LEU GLY ALA MET TYR THR LEU SEQRES 1 B 133 ARG LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP SEQRES 2 B 133 VAL GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR SEQRES 3 B 133 VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS SEQRES 4 B 133 ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU SEQRES 5 B 133 LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU SEQRES 6 B 133 PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR SEQRES 7 B 133 GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR SEQRES 8 B 133 GLY ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN SEQRES 9 B 133 LYS SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR SEQRES 10 B 133 ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP SEQRES 11 B 133 GLU ALA GLU HET FAD A 901 53 HET 6W0 A 902 21 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM 6W0 ~{N}-[3-(METHOXYMETHYL)PHENYL]-4-METHYL-THIENO[3,2- HETNAM 2 6W0 B]PYRROLE-5-CARBOXAMIDE FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 6W0 C16 H16 N2 O2 S HELIX 1 AA1 GLY A 173 SER A 181 1 9 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 SER A 201 1 6 HELIX 4 AA4 PRO A 203 ASN A 224 1 22 HELIX 5 AA5 THR A 230 GLN A 237 1 8 HELIX 6 AA6 ASP A 245 HIS A 259 1 15 HELIX 7 AA7 GLY A 287 PHE A 300 1 14 HELIX 8 AA8 ASN A 340 VAL A 349 1 10 HELIX 9 AA9 PRO A 375 GLN A 399 1 25 HELIX 10 AB1 SER A 411 GLU A 471 1 61 HELIX 11 AB2 ASP A 477 ASN A 518 1 42 HELIX 12 AB3 SER A 526 ASN A 544 1 19 HELIX 13 AB4 ASP A 557 GLU A 563 5 7 HELIX 14 AB5 SER A 576 ALA A 583 1 8 HELIX 15 AB6 PRO A 630 GLN A 636 1 7 HELIX 16 AB7 PRO A 648 MET A 658 1 11 HELIX 17 AB8 THR A 688 ARG A 692 5 5 HELIX 18 AB9 ALA A 712 GLU A 720 1 9 HELIX 19 AC1 SER A 723 GLY A 740 1 18 HELIX 20 AC2 SER A 773 GLN A 782 1 10 HELIX 21 AC3 GLY A 804 ILE A 808 5 5 HELIX 22 AC4 THR A 814 GLY A 835 1 22 HELIX 23 AC5 SER B 317 ALA B 326 1 10 HELIX 24 AC6 THR B 329 LEU B 363 1 35 HELIX 25 AC7 ILE B 367 ARG B 371 5 5 HELIX 26 AC8 THR B 384 GLY B 399 1 16 HELIX 27 AC9 ASP B 401 GLY B 410 1 10 HELIX 28 AD1 SER B 413 ARG B 425 1 13 HELIX 29 AD2 ASN B 429 ALA B 439 1 11 SHEET 1 AA1 5 ASP A 587 LYS A 589 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 589 SHEET 3 AA1 5 LYS A 280 ILE A 284 1 N VAL A 281 O ASP A 303 SHEET 4 AA1 5 ALA A 624 CYS A 627 1 O LEU A 626 N ILE A 284 SHEET 5 AA1 5 LEU A 800 PHE A 802 1 O PHE A 801 N VAL A 625 SHEET 1 AA2 2 PHE A 320 LYS A 322 0 SHEET 2 AA2 2 TYR A 325 ALA A 327 -1 O TYR A 325 N LYS A 322 SHEET 1 AA3 3 VAL A 333 VAL A 334 0 SHEET 2 AA3 3 LEU A 569 VAL A 571 -1 O LEU A 569 N VAL A 334 SHEET 3 AA3 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 570 SHEET 1 AA4 2 TYR A 363 GLU A 364 0 SHEET 2 AA4 2 VAL A 372 LYS A 373 -1 O VAL A 372 N GLU A 364 SHEET 1 AA5 2 VAL A 404 LEU A 405 0 SHEET 2 AA5 2 LYS A 408 PRO A 409 -1 O LYS A 408 N LEU A 405 SHEET 1 AA6 4 THR A 617 CYS A 622 0 SHEET 2 AA6 4 GLY A 603 ASN A 610 -1 N ALA A 608 O PHE A 618 SHEET 3 AA6 4 THR A 592 THR A 600 -1 N ARG A 595 O ILE A 607 SHEET 4 AA6 4 GLN A 642 VAL A 644 1 O GLN A 642 N VAL A 597 SHEET 1 AA7 2 GLY A 659 PHE A 660 0 SHEET 2 AA7 2 SER A 766 TYR A 767 -1 O TYR A 767 N GLY A 659 SHEET 1 AA8 5 LEU A 681 GLY A 683 0 SHEET 2 AA8 5 LEU A 697 ASN A 700 -1 O PHE A 698 N PHE A 682 SHEET 3 AA8 5 ILE A 706 VAL A 711 -1 O LEU A 708 N TRP A 699 SHEET 4 AA8 5 ASN A 664 CYS A 669 -1 N LEU A 668 O LEU A 707 SHEET 5 AA8 5 THR A 750 VAL A 752 -1 O VAL A 751 N VAL A 667 CISPEP 1 ALA A 240 PRO A 241 0 -5.22 CISPEP 2 PRO A 474 PRO A 475 0 6.39 CISPEP 3 GLN A 637 PRO A 638 0 1.24 CISPEP 4 VAL A 644 PRO A 645 0 3.97 SITE 1 AC1 32 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 32 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC1 32 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC1 32 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC1 32 VAL A 333 THR A 592 VAL A 594 THR A 628 SITE 6 AC1 32 LEU A 629 PRO A 630 TRP A 755 TRP A 760 SITE 7 AC1 32 SER A 764 TYR A 765 GLY A 804 GLU A 805 SITE 8 AC1 32 THR A 814 VAL A 815 ALA A 818 6W0 A 902 SITE 1 AC2 6 THR A 335 GLN A 358 TRP A 699 TYR A 765 SITE 2 AC2 6 ALA A 813 FAD A 901 CRYST1 120.510 180.440 235.420 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008298 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004248 0.00000