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Receptor Information

>2z3y Chain A (length=643) 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
HVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEDITAEFL
VKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQIL
DWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALA
EGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGV
LKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFG
HVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLA
ILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQP
ITPPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG

Ligand ID

F2N

InChI

InChI=1S/C36H43N9O16P2/c1-17-10-20-21(11-18(17)2)45(25(48)9-8-19-6-4-3-5-7-19)27-33(41-36(53)42-34(27)52)43(20)12-22(46)28(49)23(47)13-58-62(54,55)61-63(56,57)59-14-24-29(50)30(51)35(60-24)44-16-40-26-31(37)38-15-39-32(26)44/h3-7,10-11,15-16,22-24,28-30,35,46-47,49-51H,8-9,12-14H2,1-2H3,(H,54,55)(H,56,57)(H2,37,38,39)(H2,41,42,52,53)/t22-,23+,24+,28-,29+,30+,35+/m0/s1

InChIKey

ASOSNULLFLNYFZ-NEHYRMIBSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	Cc1cc2c(cc1C)N(C3=C(N2C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7ccccc7
CACTVS 3.341	Cc1cc2N(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=C(N(C(=O)CCc7ccccc7)c2cc1C)C(=O)NC(=O)N6
CACTVS 3.341	Cc1cc2N(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=C(N(C(=O)CCc7ccccc7)c2cc1C)C(=O)NC(=O)N6
OpenEye OEToolkits 1.5.0	Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7ccccc7
ACDLabs 10.04	O=C(N2c1cc(c(cc1N(C3=C2C(=O)NC(=O)N3)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C)CCc7ccccc7

Formula

C36 H43 N9 O16 P2

Name

[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[7,8-DIMETHYL-2,4-DIOXO-5-(3-PHENYLPROPANOYL)-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE;
1-HYDRO-5-(3-PHENYLPROPANOYL)-FLAVIN-ADENINE DINUCLEOTIDE

PDB chain

2z3y 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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Structure summary

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PDB	2z3y Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25A
Resolution	2.25 Å
Binding residue (original residue number in PDB)	G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 M332 V333 T335 V590 L625 P626 W751 W756 S760 Y761 G800 E801 A809 T810 V811 A814
Binding residue (residue number reindexed from 1)	G114 G116 S118 E137 A138 R139 G144 R145 G159 A160 M161 V162 T164 V411 L446 P447 W572 W577 S581 Y582 G612 E613 A621 T622 V623 A626
Annotation score	1

Catalytic site (original residue number in PDB)	T335 D553 K661
Catalytic site (residue number reindexed from 1)	T164 D374 K482
Enzyme Commision number	1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.

	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

PDB	RCSB:2z3y, PDBe:2z3y, PDBj:2z3y
PDBsum	2z3y
PubMed	18039463
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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Structure of PDB 2z3y Chain A Binding Site BS01