scPDB - 1ny2 entry

Protein Data Bank Entry:

PDB ID : 1ny2

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-02-11

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
2	100 %

Ligand binding site composition:

B-Factor:	20.358
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.422	317.250

% Hydrophobic	% Polar
44.68	55.32
According to VolSite

Ligand :

HET Code:	ARG_PRO_PRO_GLY
Formula:	C18H33N7O4
Molecular weight:	411.499 g/mol
DrugBank ID:	-
Buried Surface Area:	47.28 %
Polar Surface area:	180.43 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
34.4648	40.8702	3.25338

Binding mode :

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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
CG	CH2	TRP- 60	3.57	0	Hydrophobic	false
CG	CD1	LEU- 99	4.13	0	Hydrophobic	false
CZ	OD2	ASP- 189	3.78	0	Ionic (Ligand Cationic)	false
CZ	OD1	ASP- 189	3.46	0	Ionic (Ligand Cationic)	false
NH1	OD2	ASP- 189	2.73	158.77	H-Bond (Ligand Donor)	false
NH1	OD1	ASP- 189	3.18	134.95	H-Bond (Ligand Donor)	false
NH2	OD1	ASP- 189	2.76	152.66	H-Bond (Ligand Donor)	false
CB	CB	SER- 195	4.09	0	Hydrophobic	false
CG	CG1	VAL- 213	3.48	0	Hydrophobic	false
N	O	SER- 214	3	134.59	H-Bond (Ligand Donor)	false
O	N	GLY- 216	3.08	172.6	H-Bond (Protein Donor)	false
NH2	O	GLY- 219	3.21	139.9	H-Bond (Ligand Donor)	false