scPDB - 3r9h entry

Protein Data Bank Entry:

PDB ID : 3r9h

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-03-25

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:	33.020
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.023	880.875

% Hydrophobic	% Polar
47.51	52.49
According to VolSite

Ligand :

HET Code:	Z67
Formula:	C16H13F2N5O3S2
Molecular weight:	425.433 g/mol
DrugBank ID:	-
Buried Surface Area:	64.32 %
Polar Surface area:	176.82 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-65.7366	-8.65018	-47.8634

Binding mode :

What is Poseview ?

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3D View

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
S5	CG2	ILE- 10	3.92	0	Hydrophobic	false
C14	CG2	ILE- 10	3.57	0	Hydrophobic	false
C23	CG2	VAL- 18	3.7	0	Hydrophobic	false
F28	CG	LYS- 33	3.23	0	Hydrophobic	false
F28	CD2	PHE- 80	3.28	0	Hydrophobic	false
N7	O	GLU- 81	2.5	146.57	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.17	174.88	H-Bond (Protein Donor)	false
N8	O	LEU- 83	2.54	145.83	H-Bond (Ligand Donor)	false
O17	N	ASP- 86	3.11	162.76	H-Bond (Protein Donor)	false
N18	OD2	ASP- 86	2.73	152.89	H-Bond (Ligand Donor)	false
C15	CB	ASP- 86	3.87	0	Hydrophobic	false
O19	NZ	LYS- 89	3.34	172.19	H-Bond (Protein Donor)	false
S5	CD1	LEU- 134	3.69	0	Hydrophobic	false
C14	CD2	LEU- 134	4.05	0	Hydrophobic	false
F27	CB	ALA- 144	4.2	0	Hydrophobic	false
C26	CB	ASP- 145	3.21	0	Hydrophobic	false