Research workbench

Discovery of cytotoxic dolastatin 10 analogs with N-terminal modifications

Analyse Discovery of cytotoxic dolastatin 10 analogs with N-terminal modifications in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X20
Type: protein
Length: 1,840 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; Stathmin-4
UniProt: D0VWZ0, D0VWY9, P63043
Ligands: GTP, GDP, LOC, 3WY, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	429	44% helix, 16% strand	D0VWZ0
B	Tubulin beta chain	protein	428	48% helix, 17% strand	D0VWY9
C	Tubulin alpha chain	protein	430	43% helix, 17% strand	D0VWZ0
D	Tubulin beta chain	protein	430	47% helix, 17% strand	D0VWY9
E	Stathmin-4	protein	123	76% helix, 10% strand	P63043

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · 2 copies · chains A, B, C, D
3WY · 2-methyl-L-prolyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide · ligand · 2 copies · chains B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1130	0.85	0.86	115	GTP, MG, LOC
2	870	0.83	0.85	90	GTP, MG, LOC
3	1006	0.81	0.82	109	GDP, 3WY
4	456	0.72	0.82	48	empty
5	383	0.66	0.80	47	empty

Interfaces

7 interfaces between chains.

A–E · 1711 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1386 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1329 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 861 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 789 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4X20 · Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications · 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 D0VWZ0
Every structure of UniProt D0VWY9
Every structure of UniProt P63043
Elsewhere: RCSB PDB 4X20 · PDBe 4X20 · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P63043

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