Crystal structure of human thymidylate synthase delta (7-29) in complex with dump and 2-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H- PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)PHENYL)ACETIC acid

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).

Ligands and binding sites

• UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains B, D, A, C
• OF7 · [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino) phenyl]acetic acid · ligand · 4 copies · chains B, A, C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• B–D · 2183 Ų buried · 30 hydrogen bonds · protein-protein
• A–C · 258 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 201 Ų buried · 1 hydrogen bond · protein-protein
• B–A · 109 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 77 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6PF4 · Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and… · the same entry in another collection · chain B against B, 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 P04818
• Elsewhere: RCSB PDB 6PF4 · PDBe 6PF4 · UniProt P04818