Structure of PDB 5v9t Chain B Binding Site BS04

Receptor Information
>5v9t Chain B (length=593) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVE
RKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSH
YERILYPYELFQSGVSLMGVQMEVLSTDTQTSPEPGTRYTLQSFGEMADN
FKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGF
PVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLY
VGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELA
PELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHS
GFNQGYNFAEAVNFCTADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAA
DPECLDVGLAAMVCKELTLMTEEETRLRESVVQMGVLMSEEEVFELVPDD
ERQCSACRTTCFLSALTCSCNPERLVCLYHPTDLCPCPMQKKCLRYRYPL
EDLPSLLYGVKVRAQSYDTWVSVMLEDAEDRKYPENDLFRKLR
Ligand information
Ligand ID90V
InChIInChI=1S/C15H22N4O2/c1-9(2)12-7-13(18-17-12)15(21)19-6-5-11(8-19)16-14(20)10-3-4-10/h7,9-11H,3-6,8H2,1-2H3,(H,16,20)(H,17,18)/t11-/m1/s1
InChIKeyCXEXTVGTDZRKJS-LLVKDONJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.6		CC(C)c1cc([nH]n1)C(=O)N2CC[C@H](C2)NC(=O)C3CC3
CACTVS 3.385CC(C)c1cc([nH]n1)C(=O)N2CC[CH](C2)NC(=O)C3CC3
ACDLabs 12.01c1(C(C)C)nnc(c1)C(N2CCC(C2)NC(C3CC3)=O)=O
OpenEye OEToolkits 2.0.6CC(C)c1cc([nH]n1)C(=O)N2CCC(C2)NC(=O)C3CC3
FormulaC15 H22 N4 O2
NameN-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide
ChEMBLCHEMBL4088737
DrugBank
ZINCZINC000521836460
PDB chain5v9t Chain B Residue 904 [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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PDB5v9t From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		Y472 F480 H483 E485 S491 N493 K501 H571 N575 V584 N585
Binding residue
(residue number reindexed from 1)		Y300 F308 H311 E313 S319 N321 K329 H399 N403 V412 N413
Annotation score1
Binding affinityBindingDB: IC50=570nM,Kd=2400nM,EC50=960nM
Enzymatic activity
Catalytic site (original residue number in PDB) G465 Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) G293 Y300 H311 E313 H399 A411
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:5v9t, PDBe:5v9t, PDBj:5v9t
PDBsum5v9t
PubMed28512031
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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