Research workbench
Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, plp and folate- competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4- (3-(pyrrolidin-1-yl)-5-(TRIFLUOROMETHYL)PHENYL)-1,4-DIHYDROPYRANO[2, 3-C]PYRAZOLE-5-carbonitrile
Analyse Crystal structure of homo sapiens serine hydroxymethyltransferase 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V7I
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, mitochondrial
- EC
- 2.1.2.1
- UniProt
- P34897
- Ligands
- 8Z1, GLY
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 462 | 48% helix, 15% strand | P34897 |
Ligands and binding sites
- 8Z1 · (4R)-6-amino-3-methyl-4-(propan-2-yl)-4-[3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl]-1,4-dihydropyrano[2, 3-c]pyrazole-5-carbonitrile · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.75 | 0.99 | 16 | empty |
| 2 | 343 | 0.69 | 0.82 | 29 | 8Z1 |
| 3 | 324 | 0.65 | 0.80 | 32 | 8Z1, GLY |
| 4 | 62 | 0.43 | 0.83 | 17 | empty |
| 5 | 97 | 0.40 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4645 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5V7I · Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial)… · the same entry in another collection · chain A against A, TM-score 1.00
- P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · a predicted model of the same protein · chain A 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 P34897
- Elsewhere: RCSB PDB 5V7I · PDBe 5V7I · UniProt P34897
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