Structure of PDB 5v9p Chain A Binding Site BS03

Receptor Information
>5v9p Chain A (length=577) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVE
RKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSH
YERILYPYELFQSGVSLMGVQMYTLQSFGEMADNFKSDYFNMPVHMVPTE
LVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY
ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHW
SYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVT
IMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
ADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAADPECLDVGLAAMVCKE
LTLMTEEETRLRESVVQMGVLMSEEEVFELVPDDERQCSACRTTCFLSAL
TCSCNPERLVCLYHPTDLCPCPMQKKCLRYRYPLEDLPSLLYGVKVRAQS
YDTWVSVMLEDAEDRKYPENDLFRKLR
Ligand information
Ligand ID90S
InChIInChI=1S/C14H18BrN5O/c1-9(2)12-5-13(18-17-12)14(21)19-4-3-11(8-19)20-7-10(15)6-16-20/h5-7,9,11H,3-4,8H2,1-2H3,(H,17,18)/t11-/m0/s1
InChIKeyJFPBFPWCRUXYRC-NSHDSACASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)c1cc([nH]n1)C(=O)N2CC[C@@H](C2)n3cc(cn3)Br
OpenEye OEToolkits 2.0.6CC(C)c1cc([nH]n1)C(=O)N2CCC(C2)n3cc(cn3)Br
CACTVS 3.385CC(C)c1cc([nH]n1)C(=O)N2CC[CH](C2)n3cc(Br)cn3
CACTVS 3.385CC(C)c1cc([nH]n1)C(=O)N2CC[C@@H](C2)n3cc(Br)cn3
ACDLabs 12.01c3(cc(C(=O)N2CCC(n1cc(cn1)Br)C2)nn3)C(C)C
FormulaC14 H18 Br N5 O
Name[(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone
ChEMBL
DrugBank
ZINC
PDB chain5v9p Chain A Residue 904 [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]
PDB5v9p From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		W470 Y472 F480 H483 E485 N493 W503 H571 V584 N585
Binding residue
(residue number reindexed from 1)		W282 Y284 F292 H295 E297 N305 W315 H383 V396 N397
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.14,IC50=727nM
BindingDB: IC50=0.740nM
Enzymatic activity
Catalytic site (original residue number in PDB) G465 Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) G277 Y284 H295 E297 H383 A395
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
Gene Ontology

View graph for
Molecular Function
External links
PDB RCSB:5v9p, PDBe:5v9p, PDBj:5v9p
PDBsum5v9p
PubMed28512031
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

[Back to BioLiP]