scPDB - 3ig6 entry

Protein Data Bank Entry:

PDB ID : 3ig6

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 2009-07-27

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
B	78 %
D	22 %

Ligand binding site composition:

B-Factor:	19.649
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.182	1123.875

% Hydrophobic	% Polar
32.13	67.87
According to VolSite

Ligand :

HET Code:	438
Formula:	C33H37F2N5O4
Molecular weight:	605.675 g/mol
DrugBank ID:	-
Buried Surface Area:	65.41 %
Polar Surface area:	111.29 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	3
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
19.3841	-2.81011	2.74414

Binding mode :

What is Poseview ?

2D View
3D View

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
C36	CG1	VAL- 41	3.89	0	Hydrophobic	false
C31	SG	CYS- 42	3.73	0	Hydrophobic	false
O35	NE2	HIS- 57	2.84	158.21	H-Bond (Protein Donor)	false
F22	CD1	ILE- 60	3.25	0	Hydrophobic	false
C41	CD1	ILE- 60	4.31	0	Hydrophobic	false
C12	CG1	ILE- 60	3.63	0	Hydrophobic	false
F22	CD2	TYR- 94	3.67	0	Hydrophobic	false
C37	CB	SER- 95	4.06	0	Hydrophobic	false
C27	CB	SER- 95	3.57	0	Hydrophobic	false
C36	CB	ASP- 97	4.21	0	Hydrophobic	false
N1	OD1	ASP- 189	3.76	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 189	2.83	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 189	2.83	134.42	H-Bond (Ligand Donor)	false
N1	O	SER- 190	2.83	147.38	H-Bond (Ligand Donor)	false
C6	CB	SER- 190	4.03	0	Hydrophobic	false
C11	CG	GLN- 192	3.52	0	Hydrophobic	false
C12	CB	GLN- 192	3.54	0	Hydrophobic	false
C10	CB	GLN- 192	3.86	0	Hydrophobic	false
O34	N	GLY- 193	2.8	167.43	H-Bond (Protein Donor)	false
C5	CB	SER- 195	4.49	0	Hydrophobic	false
C32	CB	SER- 195	4.25	0	Hydrophobic	false
O35	OG	SER- 195	2.68	163.92	H-Bond (Protein Donor)	false
C5	CG1	VAL- 213	3.76	0	Hydrophobic	false
N1	O	GLY- 218	3.01	163.45	H-Bond (Ligand Donor)	false
C8	SG	CYS- 220	4.18	0	Hydrophobic	false
C14	SG	CYS- 220	3.44	0	Hydrophobic	false