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Structure of human dck complexed with cytarabine and ADP-mg

Analyse Structure of human dck complexed with cytarabine and ADP-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P5Z
Type: protein
Length: 229 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidine kinase
EC: 2.7.1.74
UniProt: P27707
Ligands: AR3, ADP, MG
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Deoxycytidine kinase (EC 2.7.1.74)	protein	229	59% helix, 11% strand	P27707

Ligands and binding sites

AR3 · Cytarabine · ligand · chains B
ADP · Adenosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.66	0.85	29	MG, AR3, ADP
2	71	0.33	0.75	16	empty
3	58	0.31	0.75	16	empty

Compared structures

1P5Z · Structure of human dCK complexed with cytarabine and ADP-MG · the same entry in another collection · chain B against B, TM-score 1.00
P27707 · AlphaFold monomer V2.0 prediction for deoxycytidine kinase (P27707) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P27707
Elsewhere: RCSB PDB 1P5Z · PDBe 1P5Z · UniProt P27707

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