MolNFT v1 · #32953 · protein

Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design

2C5N · Cell division protein kinase 2: “Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design”. X-ray diffraction, 1 ligand (CK8), 17 pockets (best druggability 0.81). MolNFT v1 #32953 on…

PDB: 2C5N
Type: protein
Length: 1,108 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division protein kinase 2; Cyclin A2
EC: 2.7.1.37
UniProt: P24941, P20248
Ligands: CK8
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cell division protein kinase 2 (EC 2.7.1.37)	protein	296	33% helix, 18% strand	P24941
B, D	Cyclin A2	protein	258	64% helix, 0% strand	P20248

Ligands and binding sites

CK8 · N-[4-(2,4-dimethyl-thiazol-5-yl)-pyrimidin-2-yl]-N',N'-dimethyl-benzene-1,4-diamine · ligand · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.81	0.98	24	empty
2	131	0.80	0.98	24	empty
3	899	0.76	0.79	87	empty
4	243	0.68	0.84	33	CK8
5	222	0.67	0.84	23	CK8

Interfaces

5 interfaces between chains.

A–B · 1685 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1684 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 509 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 471 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 119 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2C5N · Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug… · the same entry in another collection · chain B against B, 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 0.99
P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 2C5N · PDBe 2C5N · UniProt P24941 · UniProt P20248

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