MolNFT v1 · #53670 · protein
Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through structure guided design
2X1N · Cell division protein kinase 2: “Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through structure guided design”. X-ray diffraction, 3 ligands (X1N, ACE, NH2), 18 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2X1N
- Type
- protein
- Length
- 1,111 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2; ACE-leu-asn-pff-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- X1N, ACE, NH2
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 32% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| H | ACE-leu-asn-pff-NH2 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- X1N · 2-methyl-N-[(1Z)-3-nitrocyclohexa-2,4-dien-1-ylidene]-4,5-dihydro[1,3]thiazolo[4,5-h]quinazolin-8-amine · ligand · 2 copies · chains A, C
- ACE · Acetyl group · ligand · chains D, H
- NH2 · Amino group · ion · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.98 | 23 | empty |
| 2 | 132 | 0.80 | 0.98 | 24 | empty |
| 3 | 901 | 0.74 | 0.77 | 72 | empty |
| 4 | 222 | 0.70 | 0.86 | 25 | X1N |
| 5 | 227 | 0.68 | 0.85 | 27 | X1N |
Interfaces
6 interfaces between chains.
- A–B · 1824 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1747 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 498 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 263 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2X1N · Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure… · the same entry in another collection · chain H against H, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 2X1N · PDBe 2X1N · UniProt P24941 · UniProt P20248
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