Research workbench

CDK2/CYCLIN a in complex with compound 73

Analyse CDK2/CYCLIN a in complex with compound 73 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NEV
Type: protein
Length: 1,103 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 2; Cyclin-A2
EC: 2.7.11.22
UniProt: P24941, P20248
Ligands: 72L
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	296	35% helix, 18% strand	P24941
B, D	Cyclin-A2	protein	255	65% helix, 0% strand	P20248
C	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	297	34% helix, 17% strand	P24941

Ligands and binding sites

72L · 4-[[6-(3-phenylphenyl)-7~{H}-purin-2-yl]amino]benzenesulfonamide · ligand · 2 copies · chains A, C

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	122	0.80	0.98	24	empty
2	111	0.79	0.98	22	empty
3	1158	0.78	0.80	102	empty
4	212	0.67	0.85	23	72L
5	209	0.66	0.84	26	72L

Interfaces

5 interfaces between chains.

C–D · 1746 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1705 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 546 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 544 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 127 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5NEV · CDK2/Cyclin A in complex with compound 73 · the same entry in another collection · chain D against D, 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 A 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 5NEV · PDBe 5NEV · UniProt P24941 · UniProt P20248

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