scPDB - 2viv entry

Protein Data Bank Entry:

PDB ID : 2viv

Resolution :1.720 Å

Experimental Method : X-ray

Deposition Date : 2007-12-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Urokinase-type plasminogen activator
ID:	UROK_HUMAN
AC:	P00749
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21.73

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	18.714
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.403	610.875

% Hydrophobic	% Polar
25.41	74.59
According to VolSite

Ligand :

HET Code:	VG2
Formula:	C22H29ClN3O2
Molecular weight:	402.938 g/mol
DrugBank ID:	DB08697
Buried Surface Area:	45.67 %
Polar Surface area:	69.21 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
26.7213	10.5945	28.8492

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
CL	CB	HIS- 57	3.9	0	Hydrophobic	false
N24	OD2	ASP- 189	2.8	147.3	H-Bond (Ligand Donor)	false
N24	OD2	ASP- 189	2.8	0	Ionic (Ligand Cationic)	false
N24	OD1	ASP- 189	3.59	0	Ionic (Ligand Cationic)	false
N24	O	SER- 190	2.73	158.79	H-Bond (Ligand Donor)	false
O15	NE2	GLN- 192	3.11	141.83	H-Bond (Protein Donor)	false
C30	CB	GLN- 192	3.84	0	Hydrophobic	false
C19	CG1	VAL- 213	3.54	0	Hydrophobic	false
N24	O	GLY- 219	2.88	169.83	H-Bond (Ligand Donor)	false
C29	SG	CYS- 220	3.44	0	Hydrophobic	false