MolNFT v1 · #156494 · protein
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid
6M61: “Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid”. X-ray diffraction, 3 ligands (F4F, NAD, ZN), 11 pockets (best druggability 0.76). MolNFT v1 #156494 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6M61
- Type
- protein
- Length
- 1,334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12, 2.6.99.-
- UniProt
- P04406
- Ligands
- F4F, NAD, ZN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 336 | 31% helix, 26% strand | P04406 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 334 | 31% helix, 27% strand | P04406 |
| R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 328 | 27% helix, 23% strand | P04406 |
Ligands and binding sites
- F4F · (5aS,6R,9S,9aS)-9-methyl-9-oxidanyl-1-oxidanylidene-6-propan-2-yl-3,5a,6,7,8,9a-hexahydro-2-benzoxepine-4-carboxylic acid · ligand · 2 copies · chains O, Q
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, R, Q, P
- ZN · Zinc ion · metal · 5 copies · chains O, Q, P
- EDO · 1,2-ethanediol · additive · 11 copies · chains O, Q, P, R
- PEG · Di(hydroxyethyl)ether · additive · chains O
- GOL · Glycerol · additive · chains Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.76 | 0.83 | 63 | EDO |
| 2 | 502 | 0.75 | 0.84 | 52 | empty |
| 3 | 1146 | 0.74 | 0.77 | 119 | F4F, NAD |
| 4 | 601 | 0.69 | 0.78 | 64 | F4F, NAD |
| 5 | 635 | 0.68 | 0.77 | 76 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2027 Ų buried · 32 hydrogen bonds · protein-protein
- O–P · 2017 Ų buried · 33 hydrogen bonds · protein-protein
- Q–P · 1438 Ų buried · 23 hydrogen bonds · protein-protein
- O–R · 1434 Ų buried · 26 hydrogen bonds · protein-protein
- P–R · 460 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6M61 · Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid · the same entry in another collection · chain R against R, TM-score 1.00
- P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain Q 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 P04406
- Elsewhere: RCSB PDB 6M61 · PDBe 6M61 · UniProt P04406
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