scPDB - 3r9d entry

Protein Data Bank Entry:

PDB ID : 3r9d

Resolution :1.950 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:	33.361
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.350	1404.000

% Hydrophobic	% Polar
58.17	41.83
According to VolSite

Ligand :

HET Code:	X6B
Formula:	C16H14FN5O3S2
Molecular weight:	407.442 g/mol
DrugBank ID:	-
Buried Surface Area:	63.63 %
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
65.7761	80.376	-12.1278

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
S26	CG2	ILE- 10	4.17	0	Hydrophobic	false
C15	CG2	ILE- 10	3.53	0	Hydrophobic	false
S26	CG1	VAL- 18	4.33	0	Hydrophobic	false
C17	CG2	VAL- 18	3.72	0	Hydrophobic	false
S26	CB	ALA- 31	4.49	0	Hydrophobic	false
F25	CG	LYS- 33	3.95	0	Hydrophobic	false
C20	CD	LYS- 33	3.45	0	Hydrophobic	false
F25	CZ	PHE- 80	3.59	0	Hydrophobic	false
N04	O	GLU- 81	2.81	143.23	H-Bond (Ligand Donor)	false
N01	N	LEU- 83	3.13	171.34	H-Bond (Protein Donor)	false
N02	O	LEU- 83	2.87	125.9	H-Bond (Ligand Donor)	false
N05	OD2	ASP- 86	3.18	145.92	H-Bond (Ligand Donor)	false
O23	N	ASP- 86	3.06	167.28	H-Bond (Protein Donor)	false
C14	CB	ASP- 86	3.86	0	Hydrophobic	false
O24	NZ	LYS- 89	3.43	168.94	H-Bond (Protein Donor)	false
C15	CD2	LEU- 134	3.91	0	Hydrophobic	false
S26	CD1	LEU- 134	3.82	0	Hydrophobic	false
C19	CB	ASP- 145	3.26	0	Hydrophobic	false
O24	O	HOH- 588	3.19	155.59	H-Bond (Protein Donor)	false