MolNFT v1 · #133858 · protein
Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis bound to NADP and sddc inhibitor sddc-889
5SCV: “Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis bound to NADP and sddc inhibitor…”. X-ray diffraction, 3 ligands (NAP, H4U, CL), 3 pockets (best druggability 0.73). MolNFT v1 #133858 on GenesisL1: 3D…
- PDB
- 5SCV
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P9WNX1
- Ligands
- NAP, H4U, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 173 | 20% helix, 31% strand | P9WNX1 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 166 | 20% helix, 34% strand | P9WNX1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- H4U · 6-ethyl-5-(4-{3-[3-(1H-tetrazol-5-yl) propyl]phenoxy}butoxy)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.73 | 0.81 | 53 | empty |
| 2 | 516 | 0.72 | 0.81 | 51 | NAP, H4U, CL |
| 3 | 444 | 0.71 | 0.81 | 45 | NAP, H4U, CL |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5SCV · Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WNX1 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P9WNX1) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P9WNX1
- Elsewhere: RCSB PDB 5SCV · PDBe 5SCV · UniProt P9WNX1
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