scPDB - 1ypj entry

Protein Data Bank Entry:

PDB ID : 1ypj

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2005-01-31

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:	28.491
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.622	698.625

% Hydrophobic	% Polar
42.03	57.97
According to VolSite

Ligand :

HET Code:	UIB
Formula:	C26H34N4O3
Molecular weight:	450.573 g/mol
DrugBank ID:	-
Buried Surface Area:	60.41 %
Polar Surface area:	94.82 Å2

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

Mass center Coordinates

X	Y	Z
17.3955	-12.4649	21.6809

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
C41	CB	HIS- 57	4	0	Hydrophobic	false
C13	CZ3	TRP- 60	3.61	0	Hydrophobic	false
C41	CZ3	TRP- 60	4.28	0	Hydrophobic	false
O27	OH	TYR- 60	3.26	148.44	H-Bond (Protein Donor)	false
C18	CZ	TYR- 60	4.39	0	Hydrophobic	false
C41	CD2	TYR- 60	3.74	0	Hydrophobic	false
C28	CG	LEU- 99	4.07	0	Hydrophobic	false
C18	CD1	LEU- 99	4.21	0	Hydrophobic	false
C30	CG	LEU- 99	3.77	0	Hydrophobic	false
C24	CD1	LEU- 99	4.16	0	Hydrophobic	false
C30	CD1	ILE- 174	4.13	0	Hydrophobic	false
N1	OD1	ASP- 189	3.35	125.54	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 189	2.76	153.63	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 189	2.65	141.38	H-Bond (Ligand Donor)	false
C3	OD1	ASP- 189	3.48	0	Ionic (Ligand Cationic)	false
C3	OD2	ASP- 189	3.69	0	Ionic (Ligand Cationic)	false
C5	CG1	VAL- 213	3.9	0	Hydrophobic	false
C22	CB	TRP- 215	4.33	0	Hydrophobic	false
C32	CB	TRP- 215	3.59	0	Hydrophobic	false
O21	N	GLY- 216	3.19	159.07	H-Bond (Protein Donor)	false
N1	O	GLY- 219	2.93	160.13	H-Bond (Ligand Donor)	false