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Crystal structure of tgfbri complexed with an indolinone inhibitor

Analyse Crystal structure of tgfbri complexed with an indolinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X7O
Type: protein
Length: 1,650 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TGF-beta receptor type I
EC: 2.7.11.30
UniProt: P36897
Ligands: ZOP
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	TGF-beta receptor type I (EC 2.7.11.30)	protein	330	37% helix, 16% strand	P36897

Ligands and binding sites

ZOP · (3Z)-N-ethyl-N-methyl-2-oxo-3-(phenyl{[4-(piperidin-1-ylmethyl)phenyl]amino}methylidene)-2,3-dihydro-1H-indole-6-carboxamide · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	332	0.73	0.85	38	ZOP
2	58	0.72	0.98	19	empty
3	305	0.71	0.85	34	ZOP
4	60	0.71	0.97	21	empty
5	310	0.71	0.84	35	ZOP

Interfaces

5 interfaces between chains.

A–B · 698 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 691 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 683 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 639 Å² buried · 1 hydrogen bond · protein-protein
C–D · 626 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2X7O · Crystal structure of TGFbRI complexed with an indoli inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
P36897 · AlphaFold monomer V2.0 prediction for TGF-beta receptor type-1 (P36897) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P36897
Elsewhere: RCSB PDB 2X7O · PDBe 2X7O · UniProt P36897

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