scPDB - 3qtv entry

Protein Data Bank Entry:

PDB ID : 3qtv

Resolution :1.630 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:	15.887
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.487	327.375

% Hydrophobic	% Polar
49.48	50.52
According to VolSite

Ligand :

HET Code:	06P
Formula:	C21H28N4O2
Molecular weight:	368.473 g/mol
DrugBank ID:	-
Buried Surface Area:	61.3 %
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
16.8269	-12.4875	22.4798

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
C20	CH2	TRP- 60	3.77	0	Hydrophobic	false
C20	CZ	TYR- 60	3.56	0	Hydrophobic	false
C10	CD1	LEU- 99	4.13	0	Hydrophobic	false
C9	CD2	LEU- 99	4.01	0	Hydrophobic	false
C19	CD2	LEU- 99	4.04	0	Hydrophobic	false
C8	CD1	ILE- 174	3.72	0	Hydrophobic	false
C22	CG1	VAL- 213	3.71	0	Hydrophobic	false
N16	O	SER- 214	2.93	173.75	H-Bond (Ligand Donor)	false
C2	CE3	TRP- 215	4.36	0	Hydrophobic	false
C8	CB	TRP- 215	3.67	0	Hydrophobic	false
N4	O	GLY- 216	2.87	173.1	H-Bond (Ligand Donor)	false
O7	N	GLY- 216	2.98	166.67	H-Bond (Protein Donor)	false