MolNFT v1 · #144371 · protein

Tubulin-RB3_SLD-ttl in complex with heterocyclic pyrimidine compound 4B

6BRF · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with heterocyclic pyrimidine compound 4B”. X-ray diffraction, 6 ligands (GTP, GDP, E44), 20 pockets (best druggability 0.83). MolNFT v1 #144371 on GenesisL1: 3D structure…

PDB: 6BRF
Type: protein
Length: 2,178 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, Q9H169, E1BQ43
Ligands: GTP, GDP, E44, ACP, MG, CA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	46% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	427	48% helix, 20% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	46% helix, 16% strand	Q2XVP4
D	Tubulin beta-2B chain	protein	421	49% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	121	77% helix, 14% strand	Q9H169
F	Tubulin tyrosine ligase	protein	332	34% helix, 21% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
E44 · 2-chloro-4-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl) pyrido[3,2-d]pyrimidine · ligand · 2 copies · chains A, B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 2 copies · chains A, C
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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.83	0.84	132	GTP, MG, E44
2	407	0.83	0.91	59	E44
3	656	0.82	0.86	93	GDP, MG
4	190	0.78	0.93	35	GTP, MG
5	157	0.76	0.93	29	empty

Interfaces

9 interfaces between chains.

A–E · 1666 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1458 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1432 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 899 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 832 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6BRF · Tubulin-RB3_SLD-TTL in complex with heterocyclic pyrimidine compound 4b · the same entry in another collection · chain C against C, TM-score 1.00
Q9H169 · AlphaFold monomer V2.0 prediction for stathmin-4 (Q9H169) · a predicted model of the same protein · chain E against A, TM-score 0.76

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 Q9H169
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6BRF · PDBe 6BRF · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt Q9H169 · UniProt E1BQ43

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