Structure of PDB 5v9t Chain A Binding Site BS03

Receptor Information
>5v9t 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 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 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

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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 N493 K501 H571 N575 A583 V584 N585
Binding residue
(residue number reindexed from 1)		Y284 F292 H295 E297 N305 K313 H383 N387 A395 V396 N397
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.35,IC50=45nM
BindingDB: 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) 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:5v9t, PDBe:5v9t, PDBj:5v9t
PDBsum5v9t
PubMed28512031
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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