Structure of PDB 8frq Chain A Binding Site BS01

Receptor Information
>8frq Chain A (length=666) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNG
YSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDA
VLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVF
WDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTL
Ligand information
Ligand IDXF6
InChIInChI=1S/C40H46N12O17P2S/c1-17-10-22-23(11-18(17)2)52(27(55)9-6-20-4-7-21(8-5-20)36(59)47-40-49-48-19(3)72-40)29-35(45-39(61)46-37(29)60)50(22)12-24(53)30(56)25(54)13-66-70(62,63)69-71(64,65)67-14-26-31(57)32(58)38(68-26)51-16-44-28-33(41)42-15-43-34(28)51/h4-5,7-8,10-11,15-16,24-26,29-32,38,53-54,56-58H,6,9,12-14H2,1-3H3,(H,62,63)(H,64,65)(H2,41,42,43)(H,46,60,61)(H,47,49,59)/t24-,25+,26+,29?,30-,31+,32+,38+/m0/s1
InChIKeyOBHYXXHEJBSBHN-OHMHGEJISA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1sc(NC(=O)c2ccc(CCC(=O)N3[CH]4C(=O)NC(=O)N=C4N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]5O[CH]([CH](O)[CH]5O)n6cnc7c(N)ncnc67)c8cc(C)c(C)cc38)cc2)nn1
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3C(=O)NC(=O)N=C3N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)C(=O)CCc7ccc(cc7)C(=O)Nc8nnc(s8)C
ACDLabs 12.01Cc1nnc(NC(=O)c2ccc(CCC(=O)N3c4cc(C)c(C)cc4N(CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC4OC(n5cnc6c(N)ncnc65)C(O)C4O)C4=NC(=O)NC(=O)C43)cc2)s1
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3C(=O)NC(=O)N=C3N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O)C(=O)CCc7ccc(cc7)C(=O)Nc8nnc(s8)C
CACTVS 3.385Cc1sc(NC(=O)c2ccc(CCC(=O)N3[C@@H]4C(=O)NC(=O)N=C4N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]5O[C@H]([C@H](O)[C@@H]5O)n6cnc7c(N)ncnc67)c8cc(C)c(C)cc38)cc2)nn1
FormulaC40 H46 N12 O17 P2 S
Name[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(4aS)-7,8-dimethyl-5-(3-{4-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}propanoyl)-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain8frq Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8frq Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1
Resolution2.89 Å
Binding residue
(original residue number in PDB)
G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 V333 E559 A589 V590 L625 P626 W751 W756 S760 Y761 E801 A809 T810 V811
Binding residue
(residue number reindexed from 1)
G115 G117 S119 E138 A139 R140 G145 R146 G160 A161 V163 E389 A419 V420 L455 P456 W581 W586 S590 Y591 E631 A639 T640 V641
Annotation score1
External links
PDB RCSB:8frq, PDBe:8frq, PDBj:8frq
PDBsum8frq
PubMed
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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