scPDB - 1z71 entry

Protein Data Bank Entry:

PDB ID : 1z71

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2005-03-23

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:	18.150
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.588	658.125

% Hydrophobic	% Polar
41.03	58.97
According to VolSite

Ligand :

HET Code:	L17
Formula:	C22H20Cl2F2N4O3
Molecular weight:	497.322 g/mol
DrugBank ID:	DB04722
Buried Surface Area:	68.47 %
Polar Surface area:	92.05 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
17.1483	-13.8038	22.9858

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
CL2	CB	HIS- 57	4.03	0	Hydrophobic	false
CL2	CE2	TYR- 60	3.73	0	Hydrophobic	false
CL2	CZ3	TRP- 60	3.67	0	Hydrophobic	false
C33	CD1	LEU- 99	4.14	0	Hydrophobic	false
C6	CG	LEU- 99	3.85	0	Hydrophobic	false
C24	CD1	LEU- 99	3.78	0	Hydrophobic	false
C8	CD1	ILE- 174	4.05	0	Hydrophobic	false
C6	CG2	ILE- 174	4.4	0	Hydrophobic	false
F2	CG1	ILE- 174	3.76	0	Hydrophobic	false
F1	CD1	ILE- 174	3.47	0	Hydrophobic	false
C44	CB	ALA- 190	4.02	0	Hydrophobic	false
C7	CB	SER- 195	4.12	0	Hydrophobic	false
CL1	CG1	VAL- 213	3.69	0	Hydrophobic	false
C43	CG1	VAL- 213	3.68	0	Hydrophobic	false
N37	O	SER- 214	3.02	156.98	H-Bond (Ligand Donor)	false
C33	CB	TRP- 215	4.11	0	Hydrophobic	false
C8	CB	TRP- 215	4.07	0	Hydrophobic	false
F2	CE3	TRP- 215	3.29	0	Hydrophobic	false
N18	O	GLY- 216	2.9	156.95	H-Bond (Ligand Donor)	false
O28	N	GLY- 216	2.97	166.9	H-Bond (Protein Donor)	false
F2	CB	GLU- 217	4.44	0	Hydrophobic	false
C11	CG	GLU- 217	4.14	0	Hydrophobic	false
C50	SG	CYS- 220	4.26	0	Hydrophobic	false
CL1	CZ	TYR- 228	4.04	0	Hydrophobic	false