Structure of PDB 8ym7 Chain A Binding Site BS01

Receptor Information

>8ym7 Chain A (length=660) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWL
DNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKP
LPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRK
GNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPK
EKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKH
VKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPR
DITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLS
SRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYS
CVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVL
CTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWD
PSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDV
IVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGND
YDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREA
GRIADQFLGA

Ligand information

Ligand ID

FAD

InChI

InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1

InChIKey

VWWQXMAJTJZDQX-UYBVJOGSSA-N

SMILES

Software	SMILES
CACTVS 3.341	Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0	Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0	Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[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
CACTVS 3.341	Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04	O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C

Formula

C27 H33 N9 O15 P2

Name

FLAVIN-ADENINE DINUCLEOTIDE

PDB chain

8ym7 Chain A Residue 901 [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	8ym7 Discovery of Novel LSD1 Inhibitors for the Treatment of Autosomal Dominant Polycystic Kidney Disease
Resolution	2.83 Å
Binding residue (original residue number in PDB)	G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 A589 V590 L625 P626 W751 W756 S760 Y761 G800 E801 T810 V811 A814
Binding residue (residue number reindexed from 1)	G113 G115 S117 L135 E136 A137 R138 G143 R144 G158 A159 M160 V161 A417 V418 L453 P454 W579 W584 S588 Y589 G628 E629 T638 V639 A642
Annotation score	1

Enzymatic activity

Enzyme Commision number

1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.

External links

PDB	RCSB:8ym7, PDBe:8ym7, PDBj:8ym7
PDBsum	8ym7
PubMed
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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