scPDB - 2v3o entry

Protein Data Bank Entry:

PDB ID : 2v3o

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2007-06-19

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:	23.044
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.740	752.625

% Hydrophobic	% Polar
37.67	62.33
According to VolSite

Ligand :

HET Code:	I26
Formula:	C24H34FN4O3
Molecular weight:	445.550 g/mol
DrugBank ID:	-
Buried Surface Area:	58.09 %
Polar Surface area:	117.44 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.9599	-12.9339	21.5946

Binding mode :

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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
C21	CB	HIS- 57	4.18	0	Hydrophobic	false
C22	CZ3	TRP- 60	3.49	0	Hydrophobic	false
C24	CZ	TYR- 60	4.49	0	Hydrophobic	false
C21	CD2	TYR- 60	3.48	0	Hydrophobic	false
C24	CG	LEU- 99	4.08	0	Hydrophobic	false
C26	CG	LEU- 99	3.98	0	Hydrophobic	false
C12	CD1	LEU- 99	3.75	0	Hydrophobic	false
C18	OD2	ASP- 189	3.78	0	Ionic (Ligand Cationic)	false
C18	OD1	ASP- 189	3.69	0	Ionic (Ligand Cationic)	false
N20	OD2	ASP- 189	2.89	170.08	H-Bond (Ligand Donor)	false
N19	OD1	ASP- 189	2.87	159.24	H-Bond (Ligand Donor)	false
N14	OG	SER- 195	3.1	134	H-Bond (Ligand Donor)	false
C5	CG1	VAL- 213	3.83	0	Hydrophobic	false
C26	CD2	TRP- 215	3.81	0	Hydrophobic	false
F20	CB	TRP- 215	3.35	0	Hydrophobic	false
N20	O	GLY- 219	3	152.59	H-Bond (Ligand Donor)	false
C4	SG	CYS- 220	4.44	0	Hydrophobic	false
O16	O	HOH- 2277	2.65	179.97	H-Bond (Protein Donor)	false