Structure of PDB 5k4l Chain A Binding Site BS04

Receptor Information
>5k4l 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 ID6QN
InChIInChI=1S/C11H11N3O3/c1-2-13-10(16)8-9(15)6-3-4-12-5-7(6)14-11(8)17/h3-5H,2H2,1H3,(H,13,16)(H2,14,15,17)
InChIKeyRTMUDFJHLBNEDM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCNC(=O)C1=C(O)c2ccncc2NC1=O
OpenEye OEToolkits 2.0.5CCNC(=O)C1=C(c2ccncc2NC1=O)O
FormulaC11 H11 N3 O3
Name~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide
ChEMBLCHEMBL4441819
DrugBank
ZINCZINC000584905196
PDB chain5k4l 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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PDB5k4l Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors.
Resolution3.179 Å
Binding residue
(original residue number in PDB)		Y472 S478 F480 H483 H571
Binding residue
(residue number reindexed from 1)		Y284 S290 F292 H295 H383
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,IC50=0.05uM
BindingDB: IC50=50nM
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:5k4l, PDBe:5k4l, PDBj:5k4l
PDBsum5k4l
PubMed27499454
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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