MolNFT v1 · #85674 · protein
Rat ldha in complex with 2-((4-(4-((3-((2-methyl-1,3-benzothiazol-6YL) amino)-3-oxo-PROPYL)AMINO)-4-oxo-BUTYL)PHENYL)METHYL)PROPANEDIOIC acid
4AJO · L-lactate dehydrogenase a chain: “Rat ldha in complex with 2-((4-(4-((3-((2-methyl-1,3-benzothiazol-6YL)…”. X-ray diffraction, 1 ligand (88N), 20 pockets (best druggability 0.89). MolNFT v1 #85674 on GenesisL1: 3D structure, binding…
- PDB
- 4AJO
- Type
- protein
- Length
- 1,318 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P04642
- Ligands
- 88N
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 330 | 46% helix, 19% strand | P04642 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P04642 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 45% helix, 21% strand | P04642 |
Ligands and binding sites
- 88N · {4-[4-({3-[(2-methyl-1,3-benzothiazol-6-yl)amino]-3-oxopropyl}amino)-4-oxobutyl]benzyl}propanedioic acid · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, C
- GOL · Glycerol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.89 | 0.91 | 115 | empty |
| 2 | 163 | 0.72 | 0.90 | 26 | 88N |
| 3 | 184 | 0.70 | 0.88 | 31 | 88N |
| 4 | 243 | 0.69 | 0.85 | 39 | 88N |
| 5 | 222 | 0.69 | 0.86 | 38 | 88N |
Interfaces
6 interfaces between chains.
- C–D · 2873 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2857 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1683 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1616 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 957 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4AJO · rat LDHA in complex with 2-((4-(4-((3-((2-methyl-1,3-benzothiazol-6yl)… · the same entry in another collection · chain A against A, TM-score 1.00
- P04642 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P04642) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P04642
- Elsewhere: RCSB PDB 4AJO · PDBe 4AJO · UniProt P04642
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