MolNFT v1 · #78109 · protein
Human CDC34 E2 in complex with CC0651 inhibitor
3RZ3 · Ubiquitin-conjugating enzyme E2 R1: “Human CDC34 E2 in complex with CC0651 inhibitor”. X-ray diffraction, 1 ligand (U94), 7 pockets (best druggability 0.58). MolNFT v1 #78109 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3RZ3
- Type
- protein
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 R1
- EC
- 6.3.2.19
- UniProt
- P49427
- Ligands
- U94
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19) | protein | 164 | 36% helix, 16% strand | P49427 |
| C | Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19) | protein | 156 | 40% helix, 15% strand | P49427 |
| D | Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19) | protein | 146 | 36% helix, 18% strand | P49427 |
Ligands and binding sites
- U94 · 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.58 | 0.80 | 31 | U94 |
| 2 | 146 | 0.58 | 0.82 | 23 | U94 |
| 3 | 151 | 0.57 | 0.81 | 23 | U94 |
| 4 | 133 | 0.52 | 0.80 | 23 | U94 |
| 5 | 169 | 0.44 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 476 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 172 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P49427
- Elsewhere: RCSB PDB 3RZ3 · PDBe 3RZ3 · UniProt P49427
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