MolNFT v1 · #159714 · protein

ASK1 kinase domain in complex with compound 11

6OYW · Mitogen-activated protein kinase kinase kinase 5: “ASK1 kinase domain in complex with compound 11”. X-ray diffraction, 2 ligands (NKJ, MG), 8 pockets (best druggability 0.77). MolNFT v1 #159714 on GenesisL1: 3D structure, binding…

PDB: 6OYW
Type: protein
Length: 1,037 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: NKJ, MG
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	261	38% helix, 21% strand	Q99683
B	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	256	39% helix, 21% strand	Q99683
C	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	260	40% helix, 21% strand	Q99683
D	Mitogen-activated protein kinase kinase kinase 5 (EC 2.7.11.25)	protein	260	39% helix, 20% strand	Q99683

Ligands and binding sites

NKJ · (19S)-19-methyl-16,17,18,19-tetrahydro-8,4-(azeno)[1,2, 4]triazolo[4,3-f][1,6,13]benzoxadiazacyclohexadecin-10(9H)-one · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · chains C

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.77	0.79	110	NKJ
2	465	0.67	0.79	47	empty
3	173	0.62	0.84	24	NKJ
4	157	0.61	0.84	20	NKJ
5	147	0.60	0.84	20	NKJ

Interfaces

5 interfaces between chains.

A–B · 427 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 420 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 333 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 100 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 41 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6OYW · ASK1 kinase domain in complex with Compound 11 · the same entry in another collection · chain D against D, 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 6OYW · PDBe 6OYW · UniProt Q99683

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