scPDB - 2uuk entry

Protein Data Bank Entry:

PDB ID : 2uuk

Resolution :1.390 Å

Experimental Method : X-ray

Deposition Date : 2007-03-03

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
B	100 %

Ligand binding site composition:

B-Factor:	17.281
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.755	567.000

% Hydrophobic	% Polar
44.64	55.36
According to VolSite

Ligand :

HET Code:	897
Formula:	C26H39N4O3
Molecular weight:	455.613 g/mol
DrugBank ID:	-
Buried Surface Area:	51.39 %
Polar Surface area:	84.81 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
4.04967	18.5681	47.4677

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
C20	CB	HIS- 57	3.87	0	Hydrophobic	false
C20	CZ3	TRP- 60	3.65	0	Hydrophobic	false
C20	CD2	TYR- 60	3.67	0	Hydrophobic	false
C24	CE1	TYR- 60	4.45	0	Hydrophobic	false
C23	CG	LEU- 99	4.47	0	Hydrophobic	false
C24	CD2	LEU- 99	3.71	0	Hydrophobic	false
C19	CD1	LEU- 99	3.85	0	Hydrophobic	false
C23	CG2	ILE- 174	4.19	0	Hydrophobic	false
N4	OD2	ASP- 189	2.84	165.87	H-Bond (Ligand Donor)	false
C13	CB	ALA- 190	4.35	0	Hydrophobic	false
C13	CG1	VAL- 213	3.68	0	Hydrophobic	false
N3	O	SER- 214	2.88	172.15	H-Bond (Ligand Donor)	false
C23	CD2	TRP- 215	3.63	0	Hydrophobic	false
C16	CB	TRP- 215	3.67	0	Hydrophobic	false
O3	N	GLY- 216	3.24	155.33	H-Bond (Protein Donor)	false