scPDB - 2zf0 entry

Protein Data Bank Entry:

PDB ID : 2zf0

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-12-18

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:	15.292
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.944	445.500

% Hydrophobic	% Polar
51.52	48.48
According to VolSite

Ligand :

HET Code:	51U
Formula:	C22H28N3O2
Molecular weight:	366.477 g/mol
DrugBank ID:	DB07133
Buried Surface Area:	65 %
Polar Surface area:	77.05 Å2

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

Mass center Coordinates

X	Y	Z
16.5831	-12.2658	22.487

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
C5	CH2	TRP- 60	3.65	0	Hydrophobic	false
C5	CZ	TYR- 60	3.39	0	Hydrophobic	false
C22	CB	LEU- 99	4.07	0	Hydrophobic	false
C20	CD1	LEU- 99	3.99	0	Hydrophobic	false
C6	CD2	LEU- 99	3.96	0	Hydrophobic	false
C23	CD1	ILE- 174	4.37	0	Hydrophobic	false
C12	CB	ALA- 190	3.88	0	Hydrophobic	false
C11	CG1	VAL- 213	3.54	0	Hydrophobic	false
N3	O	SER- 214	2.66	159.93	H-Bond (Ligand Donor)	false
C1	CE3	TRP- 215	4.11	0	Hydrophobic	false
C23	CB	TRP- 215	3.6	0	Hydrophobic	false
N1	O	GLY- 216	2.68	175.09	H-Bond (Ligand Donor)	false
O1	N	GLY- 216	2.86	156.91	H-Bond (Protein Donor)	false
C1	CG	GLU- 217	4.48	0	Hydrophobic	false
C15	SG	CYS- 220	4.03	0	Hydrophobic	false
C13	CZ	TYR- 228	4.44	0	Hydrophobic	false