scPDB - 1jwt entry

Protein Data Bank Entry:

PDB ID : 1jwt

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-09-05

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
A	100 %

Ligand binding site composition:

B-Factor:	6.335
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.729	607.500

% Hydrophobic	% Polar
43.89	56.11
According to VolSite

Ligand :

HET Code:	BLI
Formula:	C22H33N6O5S
Molecular weight:	493.600 g/mol
DrugBank ID:	DB02723
Buried Surface Area:	58.32 %
Polar Surface area:	158.62 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.4043	-13.9836	23.5044

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
C06	CZ	TYR- 83	4.34	0	Hydrophobic	false
C06	CH2	TRP- 86	4.45	0	Hydrophobic	false
C06	CD1	LEU- 132	4.16	0	Hydrophobic	false
C2B	CG	LEU- 132	4.24	0	Hydrophobic	false
C4B	CG1	ILE- 209	3.45	0	Hydrophobic	false
C5B	CD1	ILE- 209	3.6	0	Hydrophobic	false
C3B	CD1	ILE- 209	3.98	0	Hydrophobic	false
C7'	CB	ALA- 230	3.99	0	Hydrophobic	false
C3'	CG1	VAL- 255	3.93	0	Hydrophobic	false
N10	O	SER- 256	3.34	123.6	H-Bond (Ligand Donor)	false
C4B	CE3	TRP- 257	3.46	0	Hydrophobic	false
O11	N	GLY- 258	2.68	144.49	H-Bond (Protein Donor)	false
N2'	O	GLY- 260	2.74	152.53	H-Bond (Ligand Donor)	false
C5'	SG	CYS- 261	4.11	0	Hydrophobic	false
O3'	OH	TYR- 270	3.29	126.37	H-Bond (Ligand Donor)	false