Structure of PDB 5ph4 Chain A Binding Site BS02

Receptor Information

>5ph4 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

8EJ

InChI

InChI=1S/C7H8N2O/c1-5-2-3-6(4-9-5)7(8)10/h2-4H,1H3,(H2,8,10)

InChIKey

IJXDURUAYOKSIS-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	Cc1ccc(cn1)C(=O)N
CACTVS 3.385	Cc1ccc(cn1)C(N)=O

Formula

C7 H8 N2 O

Name

6-methylpyridine-3-carboxamide

PDB chain

5ph4 Chain A Residue 415 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	5ph4 A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Resolution	1.269 Å
Binding residue (original residue number in PDB)	E224 A240 F241 L242 R243 Y279 S308
Binding residue (residue number reindexed from 1)	E214 A230 F231 L232 R233 Y269 S298
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:5ph4, PDBe:5ph4, PDBj:5ph4
PDBsum	5ph4
PubMed	28436492
UniProt	Q6B0I6\|KDM4D_HUMAN Lysine-specific demethylase 4D (Gene Name=KDM4D)

[Back to BioLiP]