scPDB - 4lxb entry

Protein Data Bank Entry:

PDB ID : 4lxb

Resolution :1.610 Å

Experimental Method : X-ray

Deposition Date : 2013-07-29

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:	26.703
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.599	570.375

% Hydrophobic	% Polar
42.60	57.40
According to VolSite

Ligand :

HET Code:	7R9
Formula:	C26H33ClF2N5O6S2
Molecular weight:	649.150 g/mol
DrugBank ID:	-
Buried Surface Area:	63.26 %
Polar Surface area:	166.17 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
12.0065	-13.9458	13.3227

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
C25	CH2	TRP- 60	3.44	0	Hydrophobic	false
C6	CG	LEU- 99	3.91	0	Hydrophobic	false
C1	CD1	ILE- 174	3.9	0	Hydrophobic	false
F15	CD1	ILE- 174	3.39	0	Hydrophobic	false
CL	CB	ALA- 190	3.84	0	Hydrophobic	false
S33	CB	ALA- 190	4.1	0	Hydrophobic	false
CL	CG1	VAL- 213	3.67	0	Hydrophobic	false
S33	CG1	VAL- 213	3.5	0	Hydrophobic	false
F16	CZ3	TRP- 215	3.4	0	Hydrophobic	false
C1	CD2	TRP- 215	3.43	0	Hydrophobic	false
C14	CE3	TRP- 215	4.15	0	Hydrophobic	false
O41	N	GLY- 216	3.04	163.38	H-Bond (Protein Donor)	false
N18	O	GLY- 216	2.74	125.9	H-Bond (Ligand Donor)	false
F16	CG	GLU- 217	3.86	0	Hydrophobic	false
N30	O	GLY- 219	3.09	170.44	H-Bond (Ligand Donor)	false
O39	N	GLY- 219	3.15	153.06	H-Bond (Protein Donor)	false
CL	CZ	TYR- 228	3.63	0	Hydrophobic	false
O42	O	HOH- 600	2.87	179.98	H-Bond (Protein Donor)	false