Research workbench
Synthesis of novel NAD dependant DNA ligase inhibitors via negishi cross-coupling: development of sar and resistance studies
Analyse Synthesis of novel NAD dependant DNA ligase inhibitors via negishi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UFZ
- Type
- protein
- Length
- 317 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase
- EC
- 6.5.1.2
- UniProt
- P43813
- Ligands
- IA7, IWH
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA ligase (EC 6.5.1.2) | protein | 317 | 38% helix, 21% strand | P43813 |
Ligands and binding sites
- IA7 · 5,7-bis(azanyl)-2-tert-butyl-4-(1,3-thiazol-2-yl)pyrido[2,3-d]pyrimidine-6-carbonitrile · ligand · chains A
- IWH · 1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.75 | 0.78 | 79 | IA7 |
| 2 | 195 | 0.46 | 0.75 | 34 | empty |
| 3 | 117 | 0.43 | 0.77 | 23 | IWH |
Compared structures
- 4UFZ · Synthesis of Novel NAD Dependant DNA Ligase Inhibitors via Negishi Cross-Coupling… · the same entry in another collection · chain A against A, TM-score 1.00
- P43813 · AlphaFold monomer V2.0 prediction for DNA ligase (P43813) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P43813
- Elsewhere: RCSB PDB 4UFZ · PDBe 4UFZ · UniProt P43813
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