Structure of PDB 5phb Chain A Binding Site BS02

Receptor Information

>5phb Chain A (length=331) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKAR
ETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKY
QTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTI
QDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPK
TWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIP
FNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQC
SCGEARVTFSMDAFVRILQPERYDLWKRGQD

Ligand information

Ligand ID

8P1

InChI

InChI=1S/C10H11NO/c11-8-4-5-9-7(6-8)2-1-3-10(9)12/h4-6H,1-3,11H2

InChIKey

BEVVUJBVEXJGKM-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	c1cc2c(cc1N)CCCC2=O
CACTVS 3.385	Nc1ccc2C(=O)CCCc2c1

Formula

C10 H11 N O

Name

6-azanyl-3,4-dihydro-2~{H}-naphthalen-1-one

PDB chain

5phb Chain A Residue 416 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5phb A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Resolution	1.338 Å
Binding residue (original residue number in PDB)	K94 A95 M96 L104
Binding residue (residue number reindexed from 1)	K84 A85 M86 L94
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	G174 Y181 H192 E194 H280 A292
Catalytic site (residue number reindexed from 1)	G164 Y171 H182 E184 H270 A282
Enzyme Commision number	1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.

External links

PDB	RCSB:5phb, PDBe:5phb, PDBj:5phb
PDBsum	5phb
PubMed	28436492
UniProt	Q6B0I6\|KDM4D_HUMAN Lysine-specific demethylase 4D (Gene Name=KDM4D)

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