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Human thymidylate synthase complex with dump and LY231514, a PYRROLO(2,3-D)PYRIMIDINE-based antifolate

Analyse Human thymidylate synthase complex with dump and LY231514, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JU6
Type: protein
Length: 1,144 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P04818
Ligands: UMP, LYA, PO4
Pockets: 18 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Thymidylate synthase (EC 2.1.1.45)	protein	286	33% helix, 23% strand	P04818

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
LYA · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic acid · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.77	0.87	41	UMP, LYA
2	364	0.77	0.87	39	UMP, LYA
3	368	0.76	0.87	39	UMP, LYA
4	369	0.76	0.86	40	UMP, LYA
5	184	0.53	0.79	27	empty

Interfaces

2 interfaces between chains.

A–B · 2288 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2245 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1JU6 · Human Thymidylate Synthase Complex with dUMP and LY231514, A… · the same entry in another collection · chain D against D, TM-score 1.00
P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P04818
Elsewhere: RCSB PDB 1JU6 · PDBe 1JU6 · UniProt P04818

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