Structure of PDB 6h4z Chain A

Receptor sequence
>6h4zA (length=458) Species: 9606 (Homo sapiens) [Search protein sequence]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKL
SPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFC
WHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPD
LLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFA
EAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVV
ASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKT
TCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNA
LKLRAESY
3D structure
PDB6h4z C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.
ChainA
Resolution2.3 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G184 Y191 H202 E204 H290 A302
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 C692 C695 C715 H718 C395 C398 C418 H421
BS02 ZN A C706 C708 C723 C725 C409 C411 C426 C428
BS03 MN A H499 E501 H587 H202 E204 H290
BS04 MN A N91 L413 T416 E419 N68 L117 T120 E123
BS05 FQ5 A Y425 D428 C480 W486 Y488 F496 H499 E501 K517 W519 H587 Y129 D132 C183 W189 Y191 F199 H202 E204 K220 W222 H290 MOAD: Ki=0.002uM
PDBbind-CN: -logKd/Ki=7.64,IC50=0.023uM
BindingDB: EC50=600nM,Ki=2.0nM,IC50=23nM
BS06 FQ5 A P33 Q58 T59 Y525 P10 Q35 T36 Y228 MOAD: Ki=0.002uM
PDBbind-CN: -logKd/Ki=7.64,IC50=0.023uM
BindingDB: EC50=600nM,Ki=2.0nM,IC50=23nM
External links
PDB RCSB:6h4z, PDBe:6h4z, PDBj:6h4z
PDBsum6h4z
PubMed31158747
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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