MolNFT v1 · #15920 · protein

Thymidylate synthase, mutation, N229D with 2'-deoxyuridine 5'- monophosphate (dump)

1NJD: “Thymidylate synthase, mutation, N229D with 2'-deoxyuridine 5'- monophosphate (dump)”. X-ray diffraction, 1 ligand (UMP), 1 pocket (best druggability 0.75). MolNFT v1 #15920 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1NJD
Type: protein
Length: 316 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thymidylate synthase
EC: 2.1.1.45
UniProt: P00469
Ligands: UMP
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thymidylate synthase (EC 2.1.1.45)	protein	316	41% helix, 21% strand	P00469

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	834	0.75	0.79	73	UMP

Compared structures

1NJD · Thymidylate synthase, mutation, N229D with 2'-deoxyuridine 5'-monophosphate (dump) · the same entry in another collection · chain A against A, TM-score 1.00
P00469 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P00469) · 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 P00469
Elsewhere: RCSB PDB 1NJD · PDBe 1NJD · UniProt P00469

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