MolNFT v1 · #175340 · protein

Vinorelbine in complex with tubulin

7CNN · Tubulin alpha-1B chain: “Vinorelbine in complex with tubulin”. X-ray diffraction, 6 ligands (GTP, GDP, GDF), 20 pockets (best druggability 0.81). MolNFT v1 #175340 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CNN
Type: protein
Length: 2,200 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, GDP, GDF, MG, CA, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	438	47% helix, 19% strand	Q2XVP4
B	Tubulin beta chain	protein	430	49% helix, 18% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 16% strand	Q2XVP4
D	Tubulin beta chain	protein	420	50% helix, 20% strand	A0A287AGU7
E	Stathmin-4	protein	122	77% helix, 13% strand	P63042
F	Tubulin tyrosine ligase	protein	350	31% helix, 22% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
GDF · Vinorelbine · ligand · chains B, C
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, E
CL · Chloride ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1106	0.81	0.83	116	GDP, MG, GDF
2	1153	0.80	0.82	119	GTP, MG
3	252	0.79	0.92	53	empty
4	574	0.78	0.84	63	GTP, MG
5	1053	0.73	0.77	77	empty

Interfaces

9 interfaces between chains.

A–E · 1606 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1413 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1410 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 849 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 808 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7CNN · vinorelbine in complex with tubulin · the same entry in another collection · chain C against C, TM-score 1.00
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.77

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 Q2XVP4
Every structure of UniProt A0A287AGU7
Every structure of UniProt P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7CNN · PDBe 7CNN · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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