Research workbench
Crystal structure of human thymidylate synthase delta (7-29) in complex with dump and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-PYRROLO[2, 3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)-4-chlorobenzoic acid
Analyse Crystal structure of human thymidylate synthase delta (7-29) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PF3
- Type
- protein
- Length
- 1,140 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, OE7
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, C, B, D
- OE7 · 2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-chlorobenzoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.78 | 0.87 | 44 | UMP, OE7 |
| 2 | 435 | 0.77 | 0.86 | 48 | UMP, OE7 |
| 3 | 666 | 0.77 | 0.82 | 65 | UMP, OE7 |
| 4 | 701 | 0.75 | 0.81 | 66 | UMP, OE7 |
| 5 | 128 | 0.45 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2115 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 173 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PF3 · Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and… · 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 P04818
- Elsewhere: RCSB PDB 6PF3 · PDBe 6PF3 · UniProt P04818
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