scPDB - 1v1k entry

Protein Data Bank Entry:

PDB ID : 1v1k

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2004-04-16

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:	25.676
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.103	671.625

% Hydrophobic	% Polar
54.27	45.73
According to VolSite

Ligand :

HET Code:	3FP
Formula:	C22H24F4N5O2
Molecular weight:	466.452 g/mol
DrugBank ID:	DB07054
Buried Surface Area:	47.77 %
Polar Surface area:	83.74 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
11.7341	-8.84418	9.57994

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
C2	CG2	ILE- 10	3.98	0	Hydrophobic	false
C10	CG2	ILE- 10	3.7	0	Hydrophobic	false
C14	CG2	ILE- 10	3.57	0	Hydrophobic	false
F3	CG2	VAL- 18	3.4	0	Hydrophobic	false
N1	N	LEU- 83	3.34	164	H-Bond (Protein Donor)	false
N3	O	LEU- 83	2.69	159.79	H-Bond (Ligand Donor)	false
C14	CB	ASP- 86	4.23	0	Hydrophobic	false
O1	OD2	ASP- 86	3.28	131.25	H-Bond (Ligand Donor)	false
C6	CB	ASN- 132	3.8	0	Hydrophobic	false
C2	CD1	LEU- 134	3.91	0	Hydrophobic	false
C5	CD2	LEU- 134	4.39	0	Hydrophobic	false
C15	CD2	LEU- 134	4.3	0	Hydrophobic	false
F1	CD1	LEU- 134	3.72	0	Hydrophobic	false
F1	CB	ALA- 144	3.52	0	Hydrophobic	false