scPDB - 1gz8 entry

Protein Data Bank Entry:

PDB ID : 1gz8

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2002-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent kinase 2
ID:	CDK2_HUMAN
AC:	P24941
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	18.743
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.420	486.000

% Hydrophobic	% Polar
39.58	60.42
According to VolSite

Ligand :

HET Code:	MBP
Formula:	C10H13N5O2
Molecular weight:	235.243 g/mol
DrugBank ID:	DB03663
Buried Surface Area:	61.24 %
Polar Surface area:	106.78 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
0.118	27.9669	8.27753

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C60	CG2	ILE- 10	3.49	0	Hydrophobic	false
C2'	CG2	ILE- 10	4.27	0	Hydrophobic	false
C3'	CG2	VAL- 18	3.87	0	Hydrophobic	false
C60	CG1	VAL- 18	3.94	0	Hydrophobic	false
O4'	NZ	LYS- 33	3.36	140.81	H-Bond (Protein Donor)	false
N7	NZ	LYS- 33	2.94	156.57	H-Bond (Protein Donor)	false
N9	O	GLU- 81	2.74	164.74	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.43	170.22	H-Bond (Protein Donor)	false
N2	O	LEU- 83	2.73	132.1	H-Bond (Ligand Donor)	false
O4'	O	HOH- 2167	3.31	180	H-Bond (Protein Donor)	false
O6	O	HOH- 2345	3.15	179.99	H-Bond (Protein Donor)	false