MolNFT v1 · #170537 · protein
Crystal sttructure of ZMCKO8 in complex with inhibitor 1-(3-chloro-5- trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea
6YAQ · Cytokinin dehydrogenase 8: “Crystal sttructure of ZMCKO8 in complex with inhibitor 1-(3-chloro-5…”. X-ray diffraction, 2 ligands (OHZ, FAD), 6 pockets (best druggability 0.87). MolNFT v1 #170537 on GenesisL1: 3D structure, binding…
- PDB
- 6YAQ
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin dehydrogenase 8
- EC
- 1.5.99.12
- UniProt
- E3T1X2
- Ligands
- OHZ, FAD
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 8 (EC 1.5.99.12) | protein | 499 | 36% helix, 23% strand | E3T1X2 |
Ligands and binding sites
- OHZ · 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
- IPA · Isopropyl alcohol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.87 | 0.89 | 85 | OHZ, FAD |
| 2 | 207 | 0.58 | 0.80 | 28 | EDO |
| 3 | 112 | 0.39 | 0.75 | 23 | EDO |
| 4 | 99 | 0.35 | 0.74 | 17 | empty |
| 5 | 50 | 0.31 | 0.77 | 22 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 6YAQ · Crystal sttructure of ZmCKO8 in complex with 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 E3T1X2
- Elsewhere: RCSB PDB 6YAQ · PDBe 6YAQ · UniProt E3T1X2
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