MolNFT v1 · #159711 · protein

ASK1 kinase domain in complex with gs-4997

6OYT · Mitogen-activated protein kinase kinase kinase 5: “ASK1 kinase domain in complex with gs-4997”. X-ray diffraction, 1 ligand (NJV), 10 pockets (best druggability 0.64). MolNFT v1 #159711 on GenesisL1: 3D structure, binding sites and…

PDB: 6OYT
Type: protein
Length: 949 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitogen-activated protein kinase kinase kinase 5
EC: 2.7.11.25
UniProt: Q99683
Ligands: NJV
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	222	36% helix, 24% strand	Q99683
B	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	238	34% helix, 22% strand	Q99683
C	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	236	35% helix, 23% strand	Q99683
D	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	253	34% helix, 21% strand	Q99683

Ligands and binding sites

NJV · 5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide · ligand · 4 copies · chains A, C, B, D
ACT · Acetate ion · additive · 9 copies · chains A, B, D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.64	0.85	25	NJV
2	244	0.64	0.82	43	NJV
3	257	0.62	0.81	35	NJV
4	153	0.62	0.84	24	NJV
5	450	0.60	0.75	56	ACT

Interfaces

5 interfaces between chains.

B–D · 1022 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 976 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 317 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 109 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6OYT · ASK1 kinase domain in complex with GS-4997 · the same entry in another collection · chain B against B, TM-score 1.00
Q99683 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 5… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q99683
Elsewhere: RCSB PDB 6OYT · PDBe 6OYT · UniProt Q99683

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