HEADER OXIDOREDUCTASE 26-MAY-22 7XW8 TITLE CRYSTAL STRUCTURE OF LYSINE SPECIFIC DEMETHYLASE 1 (LSD1) WITH TAK-418 TITLE 2 DISTOMER, FAD-ADDUCT 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,[HISTONE H3]-DIMETHYL-L-LYSINE(4) COMPND 6 FAD-DEPENDENT DEMETHYLASE 1A; COMPND 7 EC: 1.14.99.66; COMPND 8 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: 562 KEYWDS INHIBITOR, TAK-418, DISTOMER, FAD-ADDUCT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.OKI REVDAT 2 29-NOV-23 7XW8 1 REMARK REVDAT 1 12-OCT-22 7XW8 0 JRNL AUTH Y.HATTORI,S.MATSUMOTO,S.MORIMOTO,M.DAINI,M.TOYOFUKU, JRNL AUTH 2 S.MATSUDA,R.BABA,K.MURAKAMI,M.IWATANI,H.OKI,S.IWASAKI, JRNL AUTH 3 K.MATSUMIYA,Y.TOMINARI,H.KIMURA,M.ITO JRNL TITL DESIGN, SYNTHESIS, AND STRUCTURE-ACTIVITY RELATIONSHIP OF JRNL TITL 2 TAK-418 AND ITS DERIVATIVES AS A NOVEL SERIES OF LSD1 JRNL TITL 3 INHIBITORS WITH LOWERED RISK OF HEMATOLOGICAL SIDE EFFECTS. JRNL REF EUR.J.MED.CHEM. V. 239 14522 2022 JRNL REFN ISSN 0223-5234 JRNL PMID 35749987 JRNL DOI 10.1016/J.EJMECH.2022.114522 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 49937 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.832 REMARK 3 FREE R VALUE TEST SET COUNT : 2413 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3395 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5011 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.27900 REMARK 3 B22 (A**2) : 1.27900 REMARK 3 B33 (A**2) : -4.14900 REMARK 3 B12 (A**2) : 0.63900 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): 0.206 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.607 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5199 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7058 ; 1.132 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 636 ; 5.798 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;33.168 ;22.682 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 890 ;16.817 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.992 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 670 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3997 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2212 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3578 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 211 ; 0.130 ; 0.200 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): 2553 ; 5.701 ; 6.315 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3186 ; 7.418 ;10.598 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2646 ; 7.732 ; 7.095 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3872 ;10.504 ;11.489 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK BULK SOLVENT 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: NULL REMARK 4 REMARK 4 7XW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029763. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97645 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50185 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.40 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.30 REMARK 200 R MERGE FOR SHELL (I) : 0.93500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2Z5U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE-HCL (PH 6.5), 10% PEG REMARK 280 3350, 10% 2-METHYL-2,4-PENTANEDIOL AND 50 MM AMMONIUM FORMATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.31233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.62467 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 54.46850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 90.78083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.15617 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.31233 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 72.62467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 90.78083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.46850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 18.15617 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 169 REMARK 465 GLY A 170 REMARK 465 GLN A 460 REMARK 465 GLN A 461 REMARK 465 TYR A 462 REMARK 465 LYS A 463 REMARK 465 GLU A 464 REMARK 465 ALA A 465 REMARK 465 SER A 466 REMARK 465 GLU A 467 REMARK 465 VAL A 468 REMARK 465 LYS A 469 REMARK 465 PRO A 470 REMARK 465 PRO A 471 REMARK 465 ARG A 472 REMARK 465 ASP A 473 REMARK 465 GLY A 783 REMARK 465 PRO A 784 REMARK 465 SER A 785 REMARK 465 ILE A 786 REMARK 465 PRO A 787 REMARK 465 GLY A 788 REMARK 465 ALA A 789 REMARK 465 PRO A 790 REMARK 465 ALA A 832 REMARK 465 MET A 833 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 N5 FA8 A 904 C10 I00 A 905 2.08 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 THR A 610 1.02 -67.81 REMARK 500 LYS A 699 -35.61 83.79 REMARK 500 PRO A 701 49.84 -81.04 REMARK 500 ALA A 757 -56.60 -128.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7E0G RELATED DB: PDB REMARK 900 7E0G CONTAINS A RELATED COMPOUND IN COMPLEX WITH LSD1 DBREF 7XW8 A 172 833 UNP O60341 KDM1A_HUMAN 172 833 SEQADV 7XW8 GLY A 169 UNP O60341 EXPRESSION TAG SEQADV 7XW8 GLY A 170 UNP O60341 EXPRESSION TAG SEQADV 7XW8 SER A 171 UNP O60341 EXPRESSION TAG SEQRES 1 A 665 GLY GLY SER SER GLY VAL GLU GLY ALA ALA PHE GLN SER SEQRES 2 A 665 ARG LEU PRO HIS ASP ARG MET THR SER GLN GLU ALA ALA SEQRES 3 A 665 CYS PHE PRO ASP ILE ILE SER GLY PRO GLN GLN THR GLN SEQRES 4 A 665 LYS VAL PHE LEU PHE ILE ARG ASN ARG THR LEU GLN LEU SEQRES 5 A 665 TRP LEU ASP ASN PRO LYS ILE GLN LEU THR PHE GLU ALA SEQRES 6 A 665 THR LEU GLN GLN LEU GLU ALA PRO TYR ASN SER ASP THR SEQRES 7 A 665 VAL LEU VAL HIS ARG VAL HIS SER TYR LEU GLU ARG HIS SEQRES 8 A 665 GLY LEU ILE ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO SEQRES 9 A 665 LEU PRO THR LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SEQRES 10 A 665 SER GLY VAL SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SEQRES 11 A 665 SER PHE GLY MET ASP VAL THR LEU LEU GLU ALA ARG ASP SEQRES 12 A 665 ARG VAL GLY GLY ARG VAL ALA THR PHE ARG LYS GLY ASN SEQRES 13 A 665 TYR VAL ALA ASP LEU GLY ALA MET VAL VAL THR GLY LEU SEQRES 14 A 665 GLY GLY ASN PRO MET ALA VAL VAL SER LYS GLN VAL ASN SEQRES 15 A 665 MET GLU LEU ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR SEQRES 16 A 665 GLU ALA ASN GLY GLN ALA VAL PRO LYS GLU LYS ASP GLU SEQRES 17 A 665 MET VAL GLU GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SEQRES 18 A 665 SER TYR LEU SER HIS GLN LEU ASP PHE ASN VAL LEU ASN SEQRES 19 A 665 ASN LYS PRO VAL SER LEU GLY GLN ALA LEU GLU VAL VAL SEQRES 20 A 665 ILE GLN LEU GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE SEQRES 21 A 665 GLU HIS TRP LYS LYS ILE VAL LYS THR GLN GLU GLU LEU SEQRES 22 A 665 LYS GLU LEU LEU ASN LYS MET VAL ASN LEU LYS GLU LYS SEQRES 23 A 665 ILE LYS GLU LEU HIS GLN GLN TYR LYS GLU ALA SER GLU SEQRES 24 A 665 VAL LYS PRO PRO ARG ASP ILE THR ALA GLU PHE LEU VAL SEQRES 25 A 665 LYS SER LYS HIS ARG ASP LEU THR ALA LEU CYS LYS GLU SEQRES 26 A 665 TYR ASP GLU LEU ALA GLU THR GLN GLY LYS LEU GLU GLU SEQRES 27 A 665 LYS LEU GLN GLU LEU GLU ALA ASN PRO PRO SER ASP VAL SEQRES 28 A 665 TYR LEU SER SER ARG ASP ARG GLN ILE LEU ASP TRP HIS SEQRES 29 A 665 PHE ALA ASN LEU GLU PHE ALA ASN ALA THR PRO LEU SER SEQRES 30 A 665 THR LEU SER LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE SEQRES 31 A 665 GLU PHE THR GLY SER HIS LEU THR VAL ARG ASN GLY TYR SEQRES 32 A 665 SER CYS VAL PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE SEQRES 33 A 665 LYS LEU ASN THR ALA VAL ARG GLN VAL ARG TYR THR ALA SEQRES 34 A 665 SER GLY CYS GLU VAL ILE ALA VAL ASN THR ARG SER THR SEQRES 35 A 665 SER GLN THR PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS SEQRES 36 A 665 THR LEU PRO LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA SEQRES 37 A 665 VAL GLN PHE VAL PRO PRO LEU PRO GLU TRP LYS THR SER SEQRES 38 A 665 ALA VAL GLN ARG MET GLY PHE GLY ASN LEU ASN LYS VAL SEQRES 39 A 665 VAL LEU CYS PHE ASP ARG VAL PHE TRP ASP PRO SER VAL SEQRES 40 A 665 ASN LEU PHE GLY HIS VAL GLY SER THR THR ALA SER ARG SEQRES 41 A 665 GLY GLU LEU PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO SEQRES 42 A 665 ILE LEU LEU ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE SEQRES 43 A 665 MET GLU ASN ILE SER ASP ASP VAL ILE VAL GLY ARG CYS SEQRES 44 A 665 LEU ALA ILE LEU LYS GLY ILE PHE GLY SER SER ALA VAL SEQRES 45 A 665 PRO GLN PRO LYS GLU THR VAL VAL SER ARG TRP ARG ALA SEQRES 46 A 665 ASP PRO TRP ALA ARG GLY SER TYR SER TYR VAL ALA ALA SEQRES 47 A 665 GLY SER SER GLY ASN ASP TYR ASP LEU MET ALA GLN PRO SEQRES 48 A 665 ILE THR PRO GLY PRO SER ILE PRO GLY ALA PRO GLN PRO SEQRES 49 A 665 ILE PRO ARG LEU PHE PHE ALA GLY GLU HIS THR ILE ARG SEQRES 50 A 665 ASN TYR PRO ALA THR VAL HIS GLY ALA LEU LEU SER GLY SEQRES 51 A 665 LEU ARG GLU ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY SEQRES 52 A 665 ALA MET HET GOL A 901 6 HET MG A 902 1 HET MG A 903 1 HET FA8 A 904 53 HET I00 A 905 18 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM FA8 [[(2R,3S,4S)-5-[(4AS)-7,8-DIMETHYL-2,4-DIOXO-4A,5- HETNAM 2 FA8 DIHYDROBENZO[G]PTERIDIN-10-YL]-2,3,4-TRIHYDROXY- HETNAM 3 FA8 PENTOXY]-HYDROXY-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6- HETNAM 4 FA8 AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL HETNAM 5 FA8 HYDROGEN PHOSPHATE HETNAM I00 ~{N}-(OXAN-4-YL)-5-(3-OXIDANYLIDENEPROPYL)THIOPHENE-3- HETNAM 2 I00 CARBOXAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN I00 TAK-418 DERIVERTIVE FORMUL 2 GOL C3 H8 O3 FORMUL 3 MG 2(MG 2+) FORMUL 5 FA8 C27 H35 N9 O15 P2 FORMUL 6 I00 C13 H17 N O3 S FORMUL 7 HOH *202(H2 O) HELIX 1 AA1 SER A 171 SER A 181 1 11 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 LEU A 238 1 9 HELIX 6 AA6 PRO A 241 SER A 244 5 4 HELIX 7 AA7 ASP A 245 HIS A 259 1 15 HELIX 8 AA8 GLY A 287 PHE A 300 1 14 HELIX 9 AA9 PRO A 341 ASN A 350 1 10 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 LEU A 458 1 52 HELIX 12 AB3 THR A 475 ASP A 486 1 12 HELIX 13 AB4 ASP A 486 GLU A 512 1 27 HELIX 14 AB5 SER A 522 ALA A 541 1 20 HELIX 15 AB6 PRO A 543 LEU A 547 5 5 HELIX 16 AB7 ASP A 555 GLU A 559 5 5 HELIX 17 AB8 SER A 572 GLU A 580 1 9 HELIX 18 AB9 PRO A 626 LYS A 631 1 6 HELIX 19 AC1 PRO A 644 MET A 654 1 11 HELIX 20 AC2 GLY A 709 GLU A 716 1 8 HELIX 21 AC3 SER A 719 GLY A 736 1 18 HELIX 22 AC4 GLY A 770 GLN A 778 1 9 HELIX 23 AC5 GLY A 800 ILE A 804 5 5 HELIX 24 AC6 THR A 810 GLY A 831 1 22 SHEET 1 AA1 5 ASP A 583 LYS A 585 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 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 620 CYS A 623 1 O LEU A 622 N ILE A 284 SHEET 5 AA1 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AA2 2 THR A 319 LYS A 322 0 SHEET 2 AA2 2 TYR A 325 ASP A 328 -1 O ALA A 327 N PHE A 320 SHEET 1 AA3 3 VAL A 333 VAL A 334 0 SHEET 2 AA3 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 AA3 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 566 SHEET 1 AA4 6 LEU A 362 TYR A 363 0 SHEET 2 AA4 6 LEU A 677 HIS A 680 1 O GLY A 679 N TYR A 363 SHEET 3 AA4 6 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 4 AA4 6 ILE A 702 VAL A 707 -1 O LEU A 706 N LEU A 693 SHEET 5 AA4 6 ASN A 660 CYS A 665 -1 N LEU A 664 O LEU A 703 SHEET 6 AA4 6 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 SHEET 1 AA5 2 VAL A 400 LEU A 401 0 SHEET 2 AA5 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AA6 4 THR A 613 CYS A 618 0 SHEET 2 AA6 4 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618 SHEET 3 AA6 4 THR A 588 THR A 596 -1 N ARG A 591 O ILE A 603 SHEET 4 AA6 4 GLN A 638 VAL A 640 1 O GLN A 638 N ARG A 591 SHEET 1 AA7 2 GLY A 655 PHE A 656 0 SHEET 2 AA7 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 LINK C4X FA8 A 904 C10 I00 A 905 1555 1555 1.57 LINK OG SER A 687 MG MG A 902 1555 1555 2.91 CISPEP 1 ALA A 240 PRO A 241 0 0.39 CISPEP 2 GLN A 633 PRO A 634 0 -2.93 CISPEP 3 VAL A 640 PRO A 641 0 1.72 CRYST1 184.727 184.727 108.937 90.00 90.00 120.00 P 61 2 2 12 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 0.005413 0.003125 0.000000 0.00000 SCALE2 0.000000 0.006251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009180 0.00000