scPDB - 3biu entry

Protein Data Bank Entry:

PDB ID : 3biu

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-12-01

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:	20.802
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.772	401.625

% Hydrophobic	% Polar
51.26	48.74
According to VolSite

Ligand :

HET Code:	10U
Formula:	C20H31N5O2
Molecular weight:	373.492 g/mol
DrugBank ID:	DB06845
Buried Surface Area:	63.81 %
Polar Surface area:	117.63 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.7559	-12.306	22.4514

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
C3	CB	HIS- 57	3.92	0	Hydrophobic	false
C4	CZ	TYR- 60	3.32	0	Hydrophobic	false
C4	CH2	TRP- 60	4.13	0	Hydrophobic	false
C20	CD1	LEU- 99	3.3	0	Hydrophobic	false
C3	CD1	LEU- 99	3.93	0	Hydrophobic	false
C19	CD1	ILE- 174	4.19	0	Hydrophobic	false
C18	CG1	ILE- 174	4.2	0	Hydrophobic	false
C31	OD2	ASP- 189	3.59	0	Ionic (Ligand Cationic)	false
C31	OD1	ASP- 189	3.58	0	Ionic (Ligand Cationic)	false
N49	OD2	ASP- 189	2.73	150.84	H-Bond (Ligand Donor)	false
N48	OD2	ASP- 189	3.44	129.89	H-Bond (Ligand Donor)	false
N48	OD1	ASP- 189	2.57	151.77	H-Bond (Ligand Donor)	false
C27	CB	ALA- 190	4.48	0	Hydrophobic	false
C27	CG1	VAL- 213	3.72	0	Hydrophobic	false
N23	O	SER- 214	3.02	176.73	H-Bond (Ligand Donor)	false
C19	CD2	TRP- 215	4.05	0	Hydrophobic	false
C18	CE3	TRP- 215	3.3	0	Hydrophobic	false
C29	SG	CYS- 220	4.36	0	Hydrophobic	false
N48	O	HOH- 1012	2.98	151.43	H-Bond (Ligand Donor)	false