MolNFT v1 · #167164 · protein
Crystal structure of hsdhfr in complex with NADP+, dap, and R-naproxen
6VCJ · Dihydrofolate reductase: “Crystal structure of hsdhfr in complex with NADP+, dap, and R-naproxen”. X-ray diffraction, 4 ligands (LG3, NPX, NAP), 12 pockets (best druggability 0.75). MolNFT v1 #167164 on GenesisL1: 3D structure…
- PDB
- 6VCJ
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P00374
- Ligands
- LG3, NPX, NAP, FOL
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 184 | 23% helix, 33% strand | P00374 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 184 | 21% helix, 33% strand | P00374 |
| C | Dihydrofolate reductase (EC 1.5.1.3) | protein | 185 | 19% helix, 35% strand | P00374 |
| D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 184 | 21% helix, 35% strand | P00374 |
Ligands and binding sites
- LG3 · Pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- NPX · (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, D, C
- FOL · Folic 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.75 | 0.81 | 55 | LG3, NPX, NAP, FOL |
| 2 | 420 | 0.72 | 0.83 | 46 | LG3, NPX, NAP, FOL |
| 3 | 494 | 0.72 | 0.81 | 49 | LG3, NPX, NAP, FOL |
| 4 | 404 | 0.71 | 0.82 | 50 | LG3, NPX, NAP, FOL |
| 5 | 740 | 0.71 | 0.77 | 78 | empty |
Interfaces
5 interfaces between chains.
- A–B · 423 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 289 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VCJ · Crystal structure of hsDHFR in complex with NADP+, DAP, and R-naproxen · the same entry in another collection · chain D against D, TM-score 1.00
- P00374 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P00374) · a predicted model of the same protein · chain D 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 P00374
- Elsewhere: RCSB PDB 6VCJ · PDBe 6VCJ · UniProt P00374
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