MolNFT v1 · #147931 · protein

Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor cs-R35

6ES0 · Receptor-interacting SERINE/THREONINE-protein kinase 2: “Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor…”. X-ray diffraction, 1 ligand (BW8), 7 pockets (best…

PDB: 6ES0
Type: protein
Length: 575 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor-interacting SERINE/THREONINE-protein kinase 2
EC: 2.7.11.1, 2.7.10.2
UniProt: O43353
Ligands: BW8
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	288	39% helix, 15% strand	O43353
B	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	287	40% helix, 15% strand	O43353

Ligands and binding sites

BW8 · 2-[2-fluoranyl-4-[[2-fluoranyl-4-[2-(methylcarbamoyl) pyridin-4-yl]oxy-phenyl]carbamoylamino]phenyl]sulfanylethanoic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.81	0.82	69	empty
2	238	0.78	0.91	31	BW8
3	268	0.78	0.90	36	BW8
4	150	0.59	0.83	33	empty
5	107	0.40	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 1991 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6ES0 · Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop… · the same entry in another collection · chain A against A, TM-score 1.00
O43353 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O43353
Elsewhere: RCSB PDB 6ES0 · PDBe 6ES0 · UniProt O43353

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