scPDB - 2bvs entry

Protein Data Bank Entry:

PDB ID : 2bvs

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2005-07-04

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:	12.757
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.674	654.750

% Hydrophobic	% Polar
44.33	55.67
According to VolSite

Ligand :

HET Code:	2CE
Formula:	C24H32ClN6O5S
Molecular weight:	552.066 g/mol
DrugBank ID:	-
Buried Surface Area:	48.95 %
Polar Surface area:	208.68 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
13.2529	-14.8252	15.3496

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
C34	CB	HIS- 57	4.5	0	Hydrophobic	false
C32	CZ	TYR- 60	3.82	0	Hydrophobic	false
C34	CG	TYR- 60	3.23	0	Hydrophobic	false
C14	CH2	TRP- 60	4	0	Hydrophobic	false
C32	CH2	TRP- 60	3.69	0	Hydrophobic	false
C34	CZ3	TRP- 60	3.98	0	Hydrophobic	false
C29	CD1	LEU- 99	4.15	0	Hydrophobic	false
C31	CD1	LEU- 99	3.9	0	Hydrophobic	false
C1	CB	ALA- 190	3.99	0	Hydrophobic	false
C22	OE1	GLU- 192	3.53	0	Ionic (Ligand Cationic)	false
CL7	CG1	VAL- 213	3.78	0	Hydrophobic	false
C2	CG1	VAL- 213	3.57	0	Hydrophobic	false
O26	N	GLY- 216	3.09	175.35	H-Bond (Protein Donor)	false
O11	N	GLY- 219	3.17	149.39	H-Bond (Protein Donor)	false
C5	SG	CYS- 220	4.24	0	Hydrophobic	false
C9	SG	CYS- 220	3.37	0	Hydrophobic	false
CL7	CZ	TYR- 228	4.21	0	Hydrophobic	false