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Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1- ((9-(methylthio)-5,6-DIHYDROTHIENO[3,4-H]QUINAZOLIN-2-YL)THIO)BUTAN- 2-one, an allosteric inhibitor

Analyse Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MC1
Type: protein
Length: 881 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity protein phosphatase 10
EC: 3.1.3.16, 3.1.3.48
UniProt: Q9Y6W6
Ligands: CJA
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Dual specificity protein phosphatase 10 (EC 3.1.3.16, 3.1.3.48)	protein	147	46% helix, 16% strand	Q9Y6W6
B	Dual specificity protein phosphatase 10 (EC 3.1.3.16, 3.1.3.48)	protein	148	47% helix, 16% strand	Q9Y6W6
C	Dual specificity protein phosphatase 10 (EC 3.1.3.16, 3.1.3.48)	protein	148	47% helix, 16% strand	Q9Y6W6
D	Dual specificity protein phosphatase 10 (EC 3.1.3.16, 3.1.3.48)	protein	146	47% helix, 16% strand	Q9Y6W6
E	Dual specificity protein phosphatase 10 (EC 3.1.3.16, 3.1.3.48)	protein	145	48% helix, 16% strand	Q9Y6W6

Ligands and binding sites

CJA · 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one · ligand · 6 copies · chains A, B, C, F, D, E
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 5 copies · chains B, C, D, E, F
ACT · Acetate ion · additive · chains B, C

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

Pockets

7 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	952	0.81	0.82	72	CJA, DTT, ACT
2	418	0.79	0.87	38	CJA
3	1172	0.71	0.75	82	empty
4	176	0.56	0.80	25	empty
5	99	0.54	0.83	16	CJA

Interfaces

9 interfaces between chains.

C–F · 443 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 422 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 400 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 399 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 397 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6MC1 · Structure of MAP kinase phosphatase 5 in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
Q9Y6W6 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 10 (Q9Y6W6) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9Y6W6
Elsewhere: RCSB PDB 6MC1 · PDBe 6MC1 · UniProt Q9Y6W6

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