scPDB - 1e9h entry

Protein Data Bank Entry:

PDB ID : 1e9h

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2000-10-16

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:	47.054
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.741	523.125

% Hydrophobic	% Polar
48.39	51.61
According to VolSite

Ligand :

HET Code:	INR
Formula:	C16H9N2O5S
Molecular weight:	341.318 g/mol
DrugBank ID:	DB02519
Buried Surface Area:	65.63 %
Polar Surface area:	123.78 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
6.64271	44.7846	51.9149

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	3.33	0	Hydrophobic	false
C15	CG1	VAL- 18	4.23	0	Hydrophobic	false
C15	CB	ALA- 31	4.47	0	Hydrophobic	false
C17	CB	ALA- 31	4.28	0	Hydrophobic	false
O24	NZ	LYS- 33	2.83	145.04	H-Bond (Protein Donor)	false
O22	NZ	LYS- 33	3.23	124.64	H-Bond (Protein Donor)	false
O24	NZ	LYS- 33	2.83	0	Ionic (Protein Cationic)	false
O22	NZ	LYS- 33	3.23	0	Ionic (Protein Cationic)	false
C17	CG1	VAL- 64	4.18	0	Hydrophobic	false
C17	CG	PHE- 80	3.39	0	Hydrophobic	false
N14	O	GLU- 81	3.04	163.61	H-Bond (Ligand Donor)	false
N7	O	LEU- 83	3.1	127.65	H-Bond (Ligand Donor)	false
O13	N	LEU- 83	2.72	161.87	H-Bond (Protein Donor)	false
C4	CD	LYS- 89	3.78	0	Hydrophobic	false
C17	CD1	LEU- 134	4.21	0	Hydrophobic	false
C2	CD2	LEU- 134	4.21	0	Hydrophobic	false
C15	CD1	LEU- 134	3.52	0	Hydrophobic	false
C19	CB	ALA- 144	4.25	0	Hydrophobic	false
O24	N	ASP- 145	3.31	130.27	H-Bond (Protein Donor)	false