Structure of PDB 4uvb Chain A Binding Site BS01

Receptor Information
>4uvb 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 IDD51
InChIInChI=1S/C37H48N10O15P2/c1-17-9-21-22(10-18(17)2)47-36(3,39)11-20(19-7-5-4-6-8-19)37(47)33(43-35(54)44-34(37)53)45(21)12-23(48)27(50)24(49)13-59-63(55,56)62-64(57,58)60-14-25-28(51)29(52)32(61-25)46-16-42-26-30(38)40-15-41-31(26)46/h4-10,15-16,20,23-25,27-29,32-33,48-52H,11-14,39H2,1-3H3,(H,55,56)(H,57,58)(H2,38,40,41)(H2,43,44,53,54)/t20-,23-,24+,25+,27-,28+,29+,32+,33-,36+,37-/m0/s1
InChIKeyRMTTXOYQSVKKLC-TYNASPPKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N(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)[CH]6NC(=O)NC(=O)[C]67[CH](C[C](C)(N)N7c2cc1C)c8ccccc8
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N3C(CC(C34C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)O)O)NC(=O)NC4=O)c8ccccc8)(C)N
ACDLabs 12.01O=C4NC(=O)NC5N(c1cc(c(cc1N3C(N)(C)CC(c2ccccc2)C345)C)C)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC8OC(n7cnc6c(ncnc67)N)C(O)C8O
CACTVS 3.385Cc1cc2N(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)[C@@H]6NC(=O)NC(=O)[C@]67[C@@H](C[C@](C)(N)N7c2cc1C)c8ccccc8
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N3[C@@](CC([C@@]34[C@H](N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6ncnc7N)O)O)O)O)O)NC(=O)NC4=O)c8ccccc8)(C)N
FormulaC37 H48 N10 O15 P2
Name[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,7aS)-1-amino-1,10,11-trimethyl-4,6-dioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate
ChEMBL
DrugBank
ZINCZINC000263620981
PDB chain4uvb Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4uvb Synthesis, Biological Activity and Mechanistic Insights of 1-Substituted Cyclopropylamine Derivatives: A Novel Class of Irreversible Inhibitors of Histone Demethylase Kdm1A.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 A539 A589 V590 L625 P626 W756 S760 Y761 G800 E801 A809 T810 V811 A814
Binding residue
(residue number reindexed from 1)
G115 G117 S119 L137 E138 A139 R140 G145 R146 G160 A161 M162 V163 A369 A419 V420 L455 P456 W586 S590 Y591 G630 E631 A639 T640 V641 A644
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.49,IC50=3.26uM
Enzymatic activity
Catalytic site (original residue number in PDB) T335
Catalytic site (residue number reindexed from 1) T165
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4uvb, PDBe:4uvb, PDBj:4uvb
PDBsum4uvb
PubMed25173853
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

[Back to BioLiP]