MolNFT v1 · #107189 · protein
X-ray structure uridine phosphorylase from vibrio cholerae in complex with anticancer compound at 2.13 a resolution
4U2K: “X-ray structure uridine phosphorylase from vibrio cholerae in complex with anticancer compound at 2.13 a…”. X-ray diffraction, 2 ligands (4WR, M5F), 14 pockets (best druggability 0.78). MolNFT v1 #107189 on GenesisL1: 3D structure…
- PDB
- 4U2K
- Type
- protein
- Length
- 1,480 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q9K4U1
- Ligands
- 4WR, M5F
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 36% helix, 29% strand | Q9K4U1 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 33% helix, 29% strand | Q9K4U1 |
| C, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 27% strand | Q9K4U1 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 33% helix, 30% strand | Q9K4U1 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 33% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- 4WR · 1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B, C, D
- M5F · 1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains C, D, E, F
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains C, D, E
- PEG · Di(hydroxyethyl)ether · additive · chains D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.78 | 0.80 | 117 | EDO |
| 2 | 543 | 0.75 | 0.82 | 59 | EDO |
| 3 | 315 | 0.74 | 0.86 | 41 | GOL, M5F, 4WR |
| 4 | 453 | 0.73 | 0.83 | 50 | EDO |
| 5 | 361 | 0.72 | 0.83 | 51 | M5F |
Interfaces
12 interfaces between chains.
- A–B · 1929 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1923 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1912 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1070 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1070 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4U2K · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer… · 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 Q9K4U1
- Elsewhere: RCSB PDB 4U2K · PDBe 4U2K · UniProt Q9K4U1
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