scPDB - 1w13 entry

Protein Data Bank Entry:

PDB ID : 1w13

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-06-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.800	7.800	7.800	0.000	7.800	1

List of CHEMBLId :

CHEMBL238902

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:	26.301
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.180	293.625

% Hydrophobic	% Polar
28.74	71.26
According to VolSite

Ligand :

HET Code:	SM1
Formula:	C21H29N6O5S
Molecular weight:	477.557 g/mol
DrugBank ID:	-
Buried Surface Area:	58.77 %
Polar Surface area:	196.61 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
31.1908	9.36703	28.5221

Binding mode :

What is Poseview ?

2D View
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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
C6	CD2	LEU- 97	4.03	0	Hydrophobic	false
O3	O	LEU- 97	3.01	150.04	H-Bond (Ligand Donor)	false
O3	NE2	HIS- 99	2.86	140.88	H-Bond (Protein Donor)	false
N6	OD2	ASP- 189	2.76	127.43	H-Bond (Ligand Donor)	false
N5	OD2	ASP- 189	3.16	120.13	H-Bond (Ligand Donor)	false
N5	OD1	ASP- 189	2.89	149.3	H-Bond (Ligand Donor)	false
C18	OD2	ASP- 189	3.33	0	Ionic (Ligand Cationic)	false
C18	OD1	ASP- 189	3.85	0	Ionic (Ligand Cationic)	false
N5	OG	SER- 190	3	133.83	H-Bond (Ligand Donor)	false
C20	SG	CYS- 191	4.16	0	Hydrophobic	false
C2	CB	GLN- 192	4.04	0	Hydrophobic	false
C16	CG1	VAL- 213	3.83	0	Hydrophobic	false
N3	O	SER- 214	2.83	160.09	H-Bond (Ligand Donor)	false
N1	O	GLY- 216	2.91	150.3	H-Bond (Ligand Donor)	false
O4	N	GLY- 216	3.06	155.89	H-Bond (Protein Donor)	false
N4	O	GLY- 219	2.72	137.59	H-Bond (Ligand Donor)	false
O1	N	GLY- 219	2.89	169.61	H-Bond (Protein Donor)	false
C13	SG	CYS- 220	3.71	0	Hydrophobic	false
C20	SG	CYS- 220	3.61	0	Hydrophobic	false