scPDB - 1o0d entry

Protein Data Bank Entry:

PDB ID : 1o0d

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2003-02-21

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:	22.439
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.410	290.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	163
Formula:	C23H33N6O4
Molecular weight:	457.546 g/mol
DrugBank ID:	-
Buried Surface Area:	54.54 %
Polar Surface area:	164.38 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
16.188	19.9744	22.6712

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
C17	CD2	LEU- 99	3.92	0	Hydrophobic	false
C16	CD1	ILE- 174	4.37	0	Hydrophobic	false
C18	CD1	ILE- 174	4.48	0	Hydrophobic	false
N	OD2	ASP- 189	3.02	156.83	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 189	2.94	123.44	H-Bond (Ligand Donor)	false
C	OD1	ASP- 189	3.45	0	Ionic (Ligand Cationic)	false
C	OD2	ASP- 189	3.9	0	Ionic (Ligand Cationic)	false
C2	CB	ALA- 190	4.4	0	Hydrophobic	false
C2	CG1	VAL- 213	3.63	0	Hydrophobic	false
N3	O	SER- 214	3	149.64	H-Bond (Ligand Donor)	false
C14	CE3	TRP- 215	4.46	0	Hydrophobic	false
C16	CE3	TRP- 215	4.14	0	Hydrophobic	false
O1	N	GLY- 216	3.03	168.43	H-Bond (Protein Donor)	false
N5	O	GLY- 216	2.84	129.66	H-Bond (Ligand Donor)	false
O2	N	GLY- 219	3.3	132.68	H-Bond (Protein Donor)	false
N1	O	GLY- 219	2.99	127.37	H-Bond (Ligand Donor)	false