scPDB - 1vja entry

Protein Data Bank Entry:

PDB ID : 1vja

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.700	7.700	7.700	0.000	7.700	1

List of CHEMBLId :

CHEMBL252937

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
U	100 %

Ligand binding site composition:

B-Factor:	20.162
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.425	290.250

% Hydrophobic	% Polar
27.91	72.09
According to VolSite

Ligand :

HET Code:	7IN
Formula:	C21H28N5O6S
Molecular weight:	478.542 g/mol
DrugBank ID:	-
Buried Surface Area:	58.51 %
Polar Surface area:	204.81 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	7
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
31.3764	9.51909	28.4689

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
C19	CD2	LEU- 97	3.65	0	Hydrophobic	false
O20	O	LEU- 97	2.56	167.58	H-Bond (Ligand Donor)	false
C14	CB	SER- 146	4.46	0	Hydrophobic	false
C32	OD2	ASP- 189	3.43	0	Ionic (Ligand Cationic)	false
C32	OD1	ASP- 189	3.9	0	Ionic (Ligand Cationic)	false
N33	OD2	ASP- 189	3.09	128.55	H-Bond (Ligand Donor)	false
N33	OD1	ASP- 189	2.87	124.68	H-Bond (Ligand Donor)	false
N34	OD2	ASP- 189	2.88	133.54	H-Bond (Ligand Donor)	false
C28	CB	SER- 190	4.08	0	Hydrophobic	false
N33	OG	SER- 190	2.93	134.31	H-Bond (Ligand Donor)	false
C15	SG	CYS- 191	4.29	0	Hydrophobic	false
C16	CG	GLN- 192	3.92	0	Hydrophobic	false
C27	CG1	VAL- 213	3.57	0	Hydrophobic	false
N24	O	SER- 214	2.97	162.62	H-Bond (Ligand Donor)	false
N8	O	GLY- 216	3.14	157.84	H-Bond (Ligand Donor)	false
O21	N	GLY- 216	3.07	163.81	H-Bond (Protein Donor)	false
O18	N	GLY- 219	2.86	171.77	H-Bond (Protein Donor)	false
N34	O	GLY- 219	2.83	168.71	H-Bond (Ligand Donor)	false
C30	SG	CYS- 220	3.98	0	Hydrophobic	false
C15	SG	CYS- 220	3.47	0	Hydrophobic	false