scPDB - 1zgv entry

Protein Data Bank Entry:

PDB ID : 1zgv

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-04-22

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:	34.439
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.816	465.750

% Hydrophobic	% Polar
48.55	51.45
According to VolSite

Ligand :

HET Code:	501
Formula:	C17H21ClN6
Molecular weight:	344.842 g/mol
DrugBank ID:	DB07128
Buried Surface Area:	66.14 %
Polar Surface area:	67.14 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.421	-13.1795	22.762

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
C37	CZ	TYR- 60	3.45	0	Hydrophobic	false
C37	CH2	TRP- 60	3.64	0	Hydrophobic	false
C29	CG	LEU- 99	4.45	0	Hydrophobic	false
C29	CD1	ILE- 174	4.29	0	Hydrophobic	false
CL41	CB	ALA- 190	4.02	0	Hydrophobic	false
C5	CB	ALA- 190	3.84	0	Hydrophobic	false
C42	CG	GLU- 192	4.38	0	Hydrophobic	false
CL41	CG1	VAL- 213	3.6	0	Hydrophobic	false
C4	CG1	VAL- 213	3.66	0	Hydrophobic	false
C29	CD2	TRP- 215	3.69	0	Hydrophobic	false
C23	CE3	TRP- 215	3.36	0	Hydrophobic	false
N15	N	GLY- 216	3.23	139.61	H-Bond (Protein Donor)	false
N21	O	GLY- 216	2.71	152.39	H-Bond (Ligand Donor)	false
C42	SG	CYS- 220	3.47	0	Hydrophobic	false
CL41	CZ	TYR- 228	3.98	0	Hydrophobic	false