scPDB - 3qto entry

Protein Data Bank Entry:

PDB ID : 3qto

Resolution :1.520 Å

Experimental Method : X-ray

Deposition Date : 2011-02-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prothrombin
ID:	THRB_HUMAN
AC:	P00734
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.21.5

Chains:

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

Ligand binding site composition:

B-Factor:	14.151
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.522	337.500

% Hydrophobic	% Polar
45.00	55.00
According to VolSite

Ligand :

HET Code:	10P
Formula:	C21H28N4O2
Molecular weight:	368.473 g/mol
DrugBank ID:	-
Buried Surface Area:	65.54 %
Polar Surface area:	80.93 Å2

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

Mass center Coordinates

X	Y	Z
16.7799	-13.0396	22.3677

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
C15	CH2	TRP- 60	3.79	0	Hydrophobic	false
C15	CZ	TYR- 60	3.63	0	Hydrophobic	false
C5	CD1	LEU- 99	4.49	0	Hydrophobic	false
C6	CG	LEU- 99	3.76	0	Hydrophobic	false
C14	CD1	LEU- 99	4.08	0	Hydrophobic	false
C5	CD1	ILE- 174	3.72	0	Hydrophobic	false
C21	CG	GLU- 192	3.98	0	Hydrophobic	false
N26	O	SER- 214	2.87	175.52	H-Bond (Ligand Donor)	false
C2	CE3	TRP- 215	4.43	0	Hydrophobic	false
C5	CB	TRP- 215	3.66	0	Hydrophobic	false
N22	O	GLY- 216	2.83	174.09	H-Bond (Ligand Donor)	false
O24	N	GLY- 216	3.01	166.1	H-Bond (Protein Donor)	false
C20	SG	CYS- 220	3.9	0	Hydrophobic	false