Structure of PDB 5v9t Chain A

Receptor sequence
>5v9tA (length=577) Species: 9606 (Homo sapiens) [Search protein sequence]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVE
RKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSH
YERILYPYELFQSGVSLMGVQMYTLQSFGEMADNFKSDYFNMPVHMVPTE
LVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY
ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHW
SYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVT
IMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
ADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAADPECLDVGLAAMVCKE
LTLMTEEETRLRESVVQMGVLMSEEEVFELVPDDERQCSACRTTCFLSAL
TCSCNPERLVCLYHPTDLCPCPMQKKCLRYRYPLEDLPSLLYGVKVRAQS
YDTWVSVMLEDAEDRKYPENDLFRKLR
3D structure
PDB5v9t From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.
ChainA
Resolution3.05 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A C676 C679 C699 C488 C491 C511
BS02 ZN A C690 C692 C709 C502 C504 C521
BS03 90V A Y472 F480 H483 E485 N493 K501 H571 N575 A583 V584 N585 Y284 F292 H295 E297 N305 K313 H383 N387 A395 V396 N397 PDBbind-CN: -logKd/Ki=7.35,IC50=45nM
BindingDB: IC50=570nM,Kd=2400nM,EC50=960nM
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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