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Crystal structure of tnfalpha with isoquinoline compound 4

Analyse Crystal structure of tnfalpha with isoquinoline compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X82
Type: protein
Length: 843 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor
UniProt: P01375
Ligands: UTM
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	143	6% helix, 52% strand	P01375
B	Tumor necrosis factor	protein	139	2% helix, 51% strand	P01375
C	Tumor necrosis factor	protein	143	0% helix, 52% strand	P01375
D	Tumor necrosis factor	protein	142	6% helix, 53% strand	P01375
E	Tumor necrosis factor	protein	136	2% helix, 50% strand	P01375
F	Tumor necrosis factor	protein	140	0% helix, 52% strand	P01375

Ligands and binding sites

UTM · 8-[4-(2-{5-[(4-methylpiperazin-1-yl)methyl]-2-(1H-pyrrolo[3,2-c]pyridin-3-yl)phenoxy}ethyl) phenyl]isoquinoline · ligand · 2 copies · chains A, B, C, D, E, F

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

Pockets

11 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	502	0.84	0.90	59	UTM
2	521	0.83	0.89	63	UTM
3	644	0.77	0.83	51	empty
4	581	0.76	0.82	53	empty
5	705	0.73	0.80	60	empty

Interfaces

7 interfaces between chains.

E–F · 1213 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1165 Å² buried · 17 hydrogen bonds · protein-protein
B–E · 971 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 945 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 821 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6X82 · Crystal Structure of TNFalpha with isoquinoline compound 4 · the same entry in another collection · 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 P01375
Elsewhere: RCSB PDB 6X82 · PDBe 6X82 · UniProt P01375

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