scPDB - 2bdy entry

Protein Data Bank Entry:

PDB ID : 2bdy

Resolution :1.610 Å

Experimental Method : X-ray

Deposition Date : 2005-10-21

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:	19.205
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.905	459.000

% Hydrophobic	% Polar
51.47	48.53
According to VolSite

Ligand :

HET Code:	UNB
Formula:	C27H27N4O4S
Molecular weight:	503.593 g/mol
DrugBank ID:	-
Buried Surface Area:	59.54 %
Polar Surface area:	155.48 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
17.6138	-13.314	22.8812

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
C23	CB	HIS- 79	3.84	0	Hydrophobic	false
C23	CE1	TYR- 83	3.81	0	Hydrophobic	false
C23	CZ3	TRP- 86	3.99	0	Hydrophobic	false
C13	CD1	LEU- 132	3.99	0	Hydrophobic	false
C18	CD1	LEU- 132	3.71	0	Hydrophobic	false
C21	CD1	LEU- 132	3.65	0	Hydrophobic	false
C13	CG2	ILE- 209	3.97	0	Hydrophobic	false
C1	CD1	ILE- 209	3.8	0	Hydrophobic	false
C1	CD1	ILE- 209	3.8	0	Hydrophobic	false
C3	CD1	ILE- 209	3.54	0	Hydrophobic	false
C34	OD2	ASP- 229	3.61	0	Ionic (Ligand Cationic)	false
C34	OD1	ASP- 229	3.52	0	Ionic (Ligand Cationic)	false
N35	OD1	ASP- 229	2.64	150.32	H-Bond (Ligand Donor)	false
N36	OD2	ASP- 229	2.87	144.71	H-Bond (Ligand Donor)	false
C31	CB	ALA- 230	4	0	Hydrophobic	false
C31	CG1	VAL- 255	3.79	0	Hydrophobic	false
N25	O	SER- 256	3.06	165.11	H-Bond (Ligand Donor)	false
C6	CB	TRP- 257	4.07	0	Hydrophobic	false
C22	CB	TRP- 257	4.04	0	Hydrophobic	false
N35	O	GLY- 260	2.77	144.65	H-Bond (Ligand Donor)	false
C32	SG	CYS- 261	4.37	0	Hydrophobic	false