MolNFT v1 · #92624 · protein

Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 5

4GE5 · Tyrosine-protein phosphatase non-receptor type 9: “Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 5”. X-ray diffraction, 1 ligand (A89), 8 pockets (best druggability 0.82). MolNFT v1…

PDB: 4GE5
Type: protein
Length: 597 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 9
EC: 3.1.3.48
UniProt: P43378
Ligands: A89
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48)	protein	298	37% helix, 21% strand	P43378
B	Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48)	protein	299	35% helix, 21% strand	P43378

Ligands and binding sites

A89 · N-(4-bromo-3-methylbenzoyl)-4-[difluoro(phosphono)methyl]-L-phenylalanyl-N~5~-(3-iodobenzoyl)-L-ornithinamide · ligand · chains A

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	956	0.82	0.83	77	empty
2	223	0.56	0.79	18	empty
3	218	0.53	0.77	24	empty
4	121	0.45	0.78	21	empty
5	99	0.44	0.79	15	empty

Interfaces

1 interface between chains.

A–B · 966 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4GE5 · Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P43378 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 9… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P43378
Elsewhere: RCSB PDB 4GE5 · PDBe 4GE5 · UniProt P43378

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