scPDB - 1g5s entry

Protein Data Bank Entry:

PDB ID : 1g5s

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2000-11-02

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:	41.328
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.967	762.750

% Hydrophobic	% Polar
42.04	57.96
According to VolSite

Ligand :

HET Code:	I17
Formula:	C23H32N7
Molecular weight:	406.547 g/mol
DrugBank ID:	DB04288
Buried Surface Area:	56.74 %
Polar Surface area:	95.3 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
12.7396	-9.3623	11.4877

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
C22	CG2	ILE- 10	3.89	0	Hydrophobic	false
C21	CB	ILE- 10	3.72	0	Hydrophobic	false
C19	CD1	ILE- 10	4.39	0	Hydrophobic	false
C30	CG1	VAL- 18	3.98	0	Hydrophobic	false
C11	CG2	VAL- 18	4	0	Hydrophobic	false
C26	CB	ALA- 31	3.98	0	Hydrophobic	false
C27	CG1	VAL- 64	4.04	0	Hydrophobic	false
C26	CB	PHE- 80	3.97	0	Hydrophobic	false
C30	CD1	PHE- 80	3.49	0	Hydrophobic	false
C29	CE1	PHE- 80	3.67	0	Hydrophobic	false
C27	CG	PHE- 80	4.39	0	Hydrophobic	false
C28	CD1	PHE- 80	3.72	0	Hydrophobic	false
N7	N	LEU- 83	3.16	170.67	H-Bond (Protein Donor)	false
N18	O	LEU- 83	2.98	156.88	H-Bond (Ligand Donor)	false
N17	OD1	ASN- 132	2.85	141.99	H-Bond (Ligand Donor)	false
C27	CD1	LEU- 134	3.95	0	Hydrophobic	false
C27	CB	ALA- 144	3.78	0	Hydrophobic	false
C15	CB	ASP- 145	3.64	0	Hydrophobic	false
N17	OD1	ASP- 145	2.7	162.2	H-Bond (Ligand Donor)	false
N17	OD1	ASP- 145	2.7	0	Ionic (Ligand Cationic)	false