Research workbench
Crystal structure of hpnmt in complex with bisubstrate inhibitor N-(3- ((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4- dihydroxytetrahydrofuran-2-YL)METHYL)THIO)PROPYL)-1,2,3,4- tetrahydroisoquinoline-3-carboxamide
Analyse Crystal structure of hpnmt in complex with bisubstrate inhibitor N-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MQ4
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylethanolamine N-methyltransferase
- EC
- 2.1.1.28
- UniProt
- P11086
- Ligands
- 2D5
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 264 | 38% helix, 26% strand | P11086 |
| B | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 255 | 36% helix, 26% strand | P11086 |
Ligands and binding sites
- 2D5 · 5'-S-(3-{[(3R)-1,2,3,4-tetrahydroisoquinolin-3-ylcarbonyl]amino}propyl)-5'-thioadenosine · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 218 | 0.84 | 0.96 | 40 | 2D5, TRS |
| 2 | 243 | 0.79 | 0.92 | 48 | 2D5, TRS |
| 3 | 56 | 0.37 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MQ4 · Crystal Structure of hPNMT in Complex with bisubstrate inhibitor… · the same entry in another collection · 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 P11086
- Elsewhere: RCSB PDB 4MQ4 · PDBe 4MQ4 · UniProt P11086
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