MolNFT v1 · #179915 · protein

Crystal structure of CDK2/CYCLIN E in complex with pf-06873600

7KJS · Cyclin-dependent kinase 2: “Crystal structure of CDK2/CYCLIN E in complex with pf-06873600”. X-ray diffraction, 1 ligand (WG1), 4 pockets (best druggability 0.82). MolNFT v1 #179915 on GenesisL1: 3D structure, binding sites and…

PDB: 7KJS
Type: protein
Length: 559 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 2; G1/S-specific cyclin-E1
EC: 2.7.11.22
UniProt: P24941, P24864
Ligands: WG1
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	297	34% helix, 17% strand	P24941
B	G1/S-specific cyclin-E1	protein	262	64% helix, 1% strand	P24864

Ligands and binding sites

WG1 · 6-(difluoromethyl)-8-[(1R,2R)-2-hydroxy-2-methylcyclopentyl]-2-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.82	0.96	36	empty
2	479	0.69	0.79	56	WG1
3	360	0.67	0.81	51	empty
4	127	0.40	0.75	23	empty

Interfaces

1 interface between chains.

A–B · 1853 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

7KJS · Crystal structure of CDK2/cyclin E in complex with PF-06873600 · the same entry in another collection · chain A against A, TM-score 1.00
P24864 · AlphaFold monomer V2.0 prediction for G1/S-specific cyclin-E1 (P24864) · 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 0.88

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 P24864
Elsewhere: RCSB PDB 7KJS · PDBe 7KJS · UniProt P24941 · UniProt P24864

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