Research workbench
Crystal structure of hpnmt in complex with bisubstrate inhibitor (2R, 3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-(((2-(((7-nitro-1,2,3,4- tetrahydroisoquinolin-3-YL)METHYL)AMINO)ETHYL)THIO)METHYL) tetrahydrofuran-3,4-diol
Analyse Crystal structure of hpnmt in complex with bisubstrate inhibitor (2R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MIK
- Type
- protein
- Length
- 520 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
- JIL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 255 | 36% helix, 25% strand | P11086 |
| B | Phenylethanolamine N-methyltransferase (EC 2.1.1.28) | protein | 265 | 38% helix, 26% strand | P11086 |
Ligands and binding sites
- JIL · 9-{5-S-[2-({[(3S)-7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl]methyl}amino)ethyl]-5-thio-alpha-L-lyxofuranosyl}-9H-purin-6-amine · 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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.76 | 0.95 | 29 | JIL, TRS |
| 2 | 78 | 0.75 | 0.98 | 18 | JIL |
| 3 | 78 | 0.73 | 0.97 | 19 | JIL |
| 4 | 152 | 0.69 | 0.89 | 31 | JIL, TRS |
| 5 | 135 | 0.59 | 0.84 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 501 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4MIK · 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 4MIK · PDBe 4MIK · UniProt P11086
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