MolNFT v1 · #154050 · protein
Crystal structure of UPA_H99Y in complex with 3-azanyl-5-(azepan-1- yl)-N-[BIS(AZANYL)METHYLIDENE]-6-chloranyl-pyrazine-2-carboxamide
6JYP · Urokinase-type plasminogen activator: “Crystal structure of UPA_H99Y in complex with 3-azanyl-5-(azepan-1…”. X-ray diffraction, 2 ligands (HMX, SO4), 2 pockets (best druggability 0.35). MolNFT v1 #154050 on GenesisL1: 3D structure…
- PDB
- 6JYP
- Type
- protein
- Length
- 246 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- HMX, SO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 246 | 11% helix, 40% strand | P00749 |
Ligands and binding sites
- HMX · 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide · ligand · chains U
- SO4 · Sulfate ion · ion · chains U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.35 | 0.78 | 20 | HMX |
| 2 | 64 | 0.27 | 0.73 | 14 | SO4 |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6JYP · Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methy… · the same entry in another collection · chain U against U, 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 P00749
- Elsewhere: RCSB PDB 6JYP · PDBe 6JYP · UniProt P00749
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