Structure of PDB 5phd Chain A Binding Site BS03

Receptor Information

>5phd Chain A (length=328) 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
SCGEARVTFSMDAFVRILQPERYDLWKR

Ligand information

Ligand ID

4NC

InChI

InChI=1S/C6H5NO4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H

InChIKey

XJNPNXSISMKQEX-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	Oc1ccc(cc1O)[N+]([O-])=O
ACDLabs 10.04	[O-][N+](=O)c1cc(O)c(O)cc1
OpenEye OEToolkits 1.5.0	c1cc(c(cc1[N+](=O)[O-])O)O

Formula

C6 H5 N O4

Name

4-NITROCATECHOL

PDB chain

5phd 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	5phd A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Resolution	1.359 Å
Binding residue (original residue number in PDB)	K25 W57 Q151
Binding residue (residue number reindexed from 1)	K15 W47 Q141
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:5phd, PDBe:5phd, PDBj:5phd
PDBsum	5phd
PubMed	28436492
UniProt	Q6B0I6\|KDM4D_HUMAN Lysine-specific demethylase 4D (Gene Name=KDM4D)

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