scPDB - 4e7r entry

Protein Data Bank Entry:

PDB ID : 4e7r

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2012-03-19

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
G	100 %

Ligand binding site composition:

B-Factor:	29.292
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.680	678.375

% Hydrophobic	% Polar
37.81	62.19
According to VolSite

Ligand :

HET Code:	0NW
Formula:	C29H35Cl2N5O3S
Molecular weight:	604.591 g/mol
DrugBank ID:	-
Buried Surface Area:	60 %
Polar Surface area:	154.1 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-2.34123	-21.2057	-21.6309

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
C15	CZ3	TRP- 1060	4.04	0	Hydrophobic	false
C17	CZ3	TRP- 1060	4.25	0	Hydrophobic	false
C17	CD2	TYR- 1060	3.85	0	Hydrophobic	false
CL2	CB	ASN- 1098	4.33	0	Hydrophobic	false
C13	CD1	LEU- 1099	4.24	0	Hydrophobic	false
CL2	CG	LEU- 1099	3.81	0	Hydrophobic	false
C38	CD1	LEU- 1099	3.66	0	Hydrophobic	false
CL2	CG2	ILE- 1174	4.02	0	Hydrophobic	false
C36	CG1	ILE- 1174	4.16	0	Hydrophobic	false
C44	OD2	ASP- 1189	3.67	0	Ionic (Ligand Cationic)	false
C44	OD1	ASP- 1189	3.59	0	Ionic (Ligand Cationic)	false
N46	OD1	ASP- 1189	2.93	132.39	H-Bond (Ligand Donor)	false
N45	OD2	ASP- 1189	2.84	155.14	H-Bond (Ligand Donor)	false
N45	OD1	ASP- 1189	3.49	121.33	H-Bond (Ligand Donor)	false
C2	CB	ALA- 1190	4.2	0	Hydrophobic	false
C7	CB	GLU- 1192	4.01	0	Hydrophobic	false
C1	CG1	VAL- 1213	3.68	0	Hydrophobic	false
CL2	CE2	TRP- 1215	3.75	0	Hydrophobic	false
CL1	CE3	TRP- 1215	4.03	0	Hydrophobic	false
C37	CB	TRP- 1215	4.23	0	Hydrophobic	false
N24	O	GLY- 1216	2.79	141.78	H-Bond (Ligand Donor)	false
O10	N	GLY- 1216	2.9	163.74	H-Bond (Protein Donor)	false
CL1	CG	GLU- 1217	3.53	0	Hydrophobic	false
N45	O	GLY- 1219	2.87	129.71	H-Bond (Ligand Donor)	false
O27	N	GLY- 1219	2.72	163.01	H-Bond (Protein Donor)	false
C4	SG	CYS- 1220	4.04	0	Hydrophobic	false