Structure of PDB 3abu Chain A Binding Site BS01

Receptor Information
>3abu Chain A (length=644) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLW
LDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIK
PLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFR
KGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVP
KEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEK
HVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEITAEFLV
KSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILD
WHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAE
GLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVL
KQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGH
VGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAI
LKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPI
TPPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Ligand information
Ligand ID12F
InChIInChI=1S/C43H48FN9O17P2/c1-20-11-26-27(12-21(20)2)53-31(56)13-24(23-9-6-10-25(44)36(23)66-15-22-7-4-3-5-8-22)43(53)40(49-42(61)50-41(43)60)51(26)14-28(54)33(57)29(55)16-67-71(62,63)70-72(64,65)68-17-30-34(58)35(59)39(69-30)52-19-48-32-37(45)46-18-47-38(32)52/h3-12,18-19,24,28-31,33-35,39,54-59H,13-17H2,1-2H3,(H,62,63)(H,64,65)(H2,45,46,47)(H,50,60,61)/t24-,28+,29-,30-,31-,33+,34-,35-,39-,43+/m1/s1
InChIKeyMHNGLOZRWDKFEV-BJXRDEIQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@]34[N@@]2[C@@H](C[C@@H]4c5cccc(c5OCc6ccccc6)F)O)C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]7[C@H]([C@H]([C@@H](O7)n8cnc9c8ncnc9N)O)O)O)O)O
CACTVS 3.352Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C]67[CH](C[CH](O)N7c2cc1C)c8cccc(F)c8OCc9ccccc9
OpenEye OEToolkits 1.7.0Cc1cc2c(cc1C)N3C(CC(C34C(=O)NC(=O)N=C4N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)O)O)c8cccc(c8OCc9ccccc9)F)O
CACTVS 3.352Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)[C@]67[C@H](C[C@@H](O)N7c2cc1C)c8cccc(F)c8OCc9ccccc9
FormulaC43 H48 F N9 O17 P2
Name[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate;
[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(1R,3R,3AS)-1-HYDROXY-10,11-DIMETHYL-4,6-DIOXO-3-(3-FLUORO-2-BENZYLOXYPHENYL)-2,3,5,6-TETRAHYDRO-1H-BENZO[G] PYRROLO[2,1-E]PTERIDIN-8(4H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain3abu Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3abu Structurally Designed trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1
Resolution3.1 Å
Binding residue
(original residue number in PDB)
G285 S286 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 F538 A539 H564 A589 V590 L625 W751 W756 S760 Y761 G800 E801 A809 T810 V811 A814
Binding residue
(residue number reindexed from 1)
G114 S115 G116 S118 L136 E137 A138 R139 G144 R145 G159 A160 M161 V162 F358 A359 H384 A409 V410 L445 W571 W576 S580 Y581 G611 E612 A620 T621 V622 A625
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.62,Ki=2.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) T335 D553 K661
Catalytic site (residue number reindexed from 1) T164 D373 K481
Enzyme Commision number 1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
Cellular Component
GO:0005634 nucleus

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3abu, PDBe:3abu, PDBj:3abu
PDBsum3abu
PubMed20568732
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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