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GRB2 SH2 domain with compound 7

Analyse GRB2 SH2 domain with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MPH
Type: protein
Length: 563 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Growth factor receptor-bound protein 2
UniProt: P62993
Ligands: ZLY, SO4
Pockets: 7 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Growth factor receptor-bound protein 2	protein	90	18% helix, 28% strand	P62993
B	Growth factor receptor-bound protein 2	protein	94	18% helix, 29% strand	P62993
C, D, E	Growth factor receptor-bound protein 2	protein	95	20% helix, 32% strand	P62993
F	Growth factor receptor-bound protein 2	protein	94	20% helix, 28% strand	P62993

Ligands and binding sites

ZLY · (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 11 copies · chains A, E, B, C, D, F
EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	518	0.66	0.77	52	EDO
2	475	0.61	0.75	37	ZLY
3	69	0.53	0.86	22	empty
4	239	0.53	0.76	29	EDO
5	234	0.51	0.75	28	empty

Interfaces

6 interfaces between chains.

C–D · 1460 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 479 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 126 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 113 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7MPH · GRB2 SH2 Domain with Compound 7 · the same entry in another collection · chain F against F, TM-score 1.00
P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P62993
Elsewhere: RCSB PDB 7MPH · PDBe 7MPH · UniProt P62993

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