scPDB - 4fkv entry

Protein Data Bank Entry:

PDB ID : 4fkv

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2012-06-13

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:	35.275
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.042	678.375

% Hydrophobic	% Polar
49.25	50.75
According to VolSite

Ligand :

HET Code:	61K
Formula:	C20H19N7O4S
Molecular weight:	453.474 g/mol
DrugBank ID:	-
Buried Surface Area:	61.12 %
Polar Surface area:	179.8 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-12.416	-8.8085	-10.2015

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
CAX	CD1	ILE- 10	4.25	0	Hydrophobic	false
CAP	CG2	VAL- 18	3.8	0	Hydrophobic	false
CAY	CG2	VAL- 18	4.28	0	Hydrophobic	false
CAN	CG1	VAL- 18	4.04	0	Hydrophobic	false
CAK	CB	ALA- 31	4.16	0	Hydrophobic	false
CBE	CB	ALA- 31	4.15	0	Hydrophobic	false
OAB	NZ	LYS- 33	2.79	161.57	H-Bond (Protein Donor)	false
CAK	CG1	VAL- 64	4	0	Hydrophobic	false
CAK	CB	PHE- 80	3.57	0	Hydrophobic	false
N4	O	GLU- 81	2.9	164.69	H-Bond (Ligand Donor)	false
N8	O	LEU- 83	3.46	135.69	H-Bond (Ligand Donor)	false
OAC	N	LEU- 83	2.89	169.87	H-Bond (Protein Donor)	false
OAE	N	ASP- 86	2.99	156.9	H-Bond (Protein Donor)	false
CAH	CB	ASP- 86	3.76	0	Hydrophobic	false
CAF	CD2	LEU- 134	3.98	0	Hydrophobic	false
CBE	CD1	LEU- 134	3.65	0	Hydrophobic	false
CAJ	CB	ALA- 144	4.05	0	Hydrophobic	false