MolNFT v1 · #125231 · protein

The X-ray co-crystal structure of human CDK2/CYCLINE and dinaciclib.

5L2W · Cyclin-dependent kinase 2: “The X-ray co-crystal structure of human CDK2/CYCLINE and dinaciclib.”. X-ray diffraction, 1 ligand (1QK), 6 pockets (best druggability 0.81). MolNFT v1 #125231 on GenesisL1: 3D structure, binding sites…

PDB: 5L2W
Type: protein
Length: 568 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: 1QK
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	298	34% helix, 16% strand	P24941
B	G1/S-specific cyclin-E1	protein	270	61% helix, 1% strand	P24864

Ligands and binding sites

1QK · 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium · ligand · chains A
GOL · Glycerol · additive · chains A

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

Pockets

6 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	271	0.81	0.93	43	empty
2	200	0.70	0.87	26	1QK
3	201	0.62	0.82	38	empty
4	152	0.43	0.75	29	empty
5	112	0.38	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 1922 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

5L2W · The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib. · 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 5L2W · PDBe 5L2W · UniProt P24941 · UniProt P24864

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