Structure of PDB 5ceh Chain A Binding Site BS03

Receptor Information
>5ceh 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 ID50P
InChIInChI=1S/C16H14N4O/c1-10(2)13-14(11-6-4-3-5-7-11)19-15-12(8-17)9-18-20(15)16(13)21/h3-7,9-10,19H,1-2H3
InChIKeyDHXKRMSKXLDZGY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C2(C(C)C)=C(c1ccccc1)Nc3n(C2=O)ncc3C#N
OpenEye OEToolkits 1.9.2CC(C)C1=C(Nc2c(cnn2C1=O)C#N)c3ccccc3
CACTVS 3.385CC(C)C1=C(Nc2n(ncc2C#N)C1=O)c3ccccc3
FormulaC16 H14 N4 O
Name7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
ChEMBLCHEMBL4454253
DrugBank
ZINCZINC000328578212
PDB chain5ceh 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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PDB5ceh An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells.
Resolution3.14 Å
Binding residue
(original residue number in PDB)		Y409 A411 Y472 F480 H483 K501 H571 N575
Binding residue
(residue number reindexed from 1)		Y221 A223 Y284 F292 H295 K313 H383 N387
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.00,IC50=10nM
BindingDB: IC50=10.0nM,EC50=5200nM
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:5ceh, PDBe:5ceh, PDBj:5ceh
PDBsum5ceh
PubMed27214401
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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