MolNFT v1 · #154585 · protein
Human MTHFD2 in complex with compound 18
6KG2 · Bifunctional methylenetetrahydrofolate…: “Human MTHFD2 in complex with compound 18”. X-ray diffraction, 3 ligands (D8C, NAD, PO4), 5 pockets (best druggability 0.68). MolNFT v1 #154585 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KG2
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial
- EC
- 1.5.1.15, 3.5.4.9
- UniProt
- P13995
- Ligands
- D8C, NAD, PO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 293 | 41% helix, 15% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 290 | 41% helix, 16% strand | P13995 |
Ligands and binding sites
- D8C · N-[2-chloranyl-4-[[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxidanylidene-2,4-dihydro-1H-chromeno[3,4-c]pyridin-3-yl]carbonyl]phenyl]methanesulfonamide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.68 | 0.77 | 75 | D8C, NAD, PO4 |
| 2 | 500 | 0.66 | 0.77 | 59 | D8C, NAD, PO4 |
| 3 | 99 | 0.38 | 0.74 | 15 | empty |
| 4 | 94 | 0.37 | 0.75 | 17 | empty |
| 5 | 68 | 0.31 | 0.75 | 19 | NAD, PO4 |
Interfaces
1 interface between chains.
- A–B · 1596 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
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 P13995
- Elsewhere: RCSB PDB 6KG2 · PDBe 6KG2 · UniProt P13995
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