scPDB - 3rai entry

Protein Data Bank Entry:

PDB ID : 3rai

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-03-28

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:	24.623
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.763	624.375

% Hydrophobic	% Polar
42.70	57.30
According to VolSite

Ligand :

HET Code:	X85
Formula:	C20H27N6O4
Molecular weight:	415.466 g/mol
DrugBank ID:	-
Buried Surface Area:	52.58 %
Polar Surface area:	139.52 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-64.6602	-44.9476	-9.4501

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
C5	CD1	ILE- 10	4.37	0	Hydrophobic	false
C30	CG2	ILE- 10	4.39	0	Hydrophobic	false
C16	CG2	ILE- 10	3.34	0	Hydrophobic	false
C1	CG2	ILE- 10	3.73	0	Hydrophobic	false
C4	CG1	VAL- 18	4.28	0	Hydrophobic	false
C4	CB	ALA- 31	4.08	0	Hydrophobic	false
O11	NZ	LYS- 33	2.7	0	Ionic (Protein Cationic)	false
N8	O	GLU- 81	3.11	178.66	H-Bond (Ligand Donor)	false
O9	N	LEU- 83	2.9	172.23	H-Bond (Protein Donor)	false
N13	O	LEU- 83	2.87	128.89	H-Bond (Ligand Donor)	false
N21	OD2	ASP- 86	2.8	136.94	H-Bond (Ligand Donor)	false
N21	OD2	ASP- 86	2.8	0	Ionic (Ligand Cationic)	false
C23	CD	LYS- 88	3.71	0	Hydrophobic	false
C19	CB	LYS- 89	3.42	0	Hydrophobic	false
C1	CD2	LEU- 134	4.07	0	Hydrophobic	false
C14	CD2	LEU- 134	3.96	0	Hydrophobic	false
C5	CD1	LEU- 134	3.54	0	Hydrophobic	false
N15	O	HOH- 619	3.14	138.09	H-Bond (Ligand Donor)	false