Research workbench
Human MTHFD2 in complex with compound 21 and 9
Analyse Human MTHFD2 in complex with compound 21 and 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EHN
- Type
- protein
- Length
- 566 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
- J4F, J49
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% 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 | 282 | 44% helix, 16% strand | P13995 |
| B | Bifunctional methylenetetrahydrofolate DEHYDROGENASE/CYCLOHYDROLASE, mitochondrial (EC 1.5.1.15, 3.5.4.9) | protein | 284 | 46% helix, 17% strand | P13995 |
Ligands and binding sites
- J4F · 3-[4-[[1-[(4-chloranyl-1H-indol-2-yl)methyl]-3,7-dimethyl-2,6-bis(oxidanylidene)purin-8-yl]amino]-6-methyl-pyrimidin-2-yl]propanoic acid · ligand · 2 copies · chains A, B
- J49 · (2S)-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl) carbamoylamino]phenyl]carbonylamino]pentanedioic acid · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.77 | 0.81 | 65 | J4F, J49 |
| 2 | 703 | 0.76 | 0.81 | 64 | J4F, J49 |
| 3 | 53 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1659 Ų buried · 29 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 7EHN · PDBe 7EHN · UniProt P13995
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