scPDB - 1ypm entry

Protein Data Bank Entry:

PDB ID : 1ypm

Resolution :1.850 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:	27.489
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.662	519.750

% Hydrophobic	% Polar
44.16	55.84
According to VolSite

Ligand :

HET Code:	RA4
Formula:	C23H36N7O5
Molecular weight:	490.576 g/mol
DrugBank ID:	DB04771
Buried Surface Area:	57.49 %
Polar Surface area:	187.96 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
16.7225	-14.1818	22.9065

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
C13	CB	HIS- 57	4.17	0	Hydrophobic	false
C14	CZ	TYR- 60	3.29	0	Hydrophobic	false
C13	CZ3	TRP- 60	3.96	0	Hydrophobic	false
C14	CH2	TRP- 60	3.85	0	Hydrophobic	false
C19	CG	LEU- 99	4.01	0	Hydrophobic	false
C13	CD1	LEU- 99	4.07	0	Hydrophobic	false
C19	CG2	ILE- 174	4.06	0	Hydrophobic	false
C20	CG1	ILE- 174	3.61	0	Hydrophobic	false
C2	OD1	ASP- 189	3.38	0	Ionic (Ligand Cationic)	false
C2	OD2	ASP- 189	3.53	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 189	2.73	140.49	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 189	3.26	124.39	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 189	2.62	140.36	H-Bond (Ligand Donor)	false
C5	CB	ALA- 190	4.29	0	Hydrophobic	false
C7	CG1	VAL- 213	4.3	0	Hydrophobic	false
C5	CG1	VAL- 213	3.99	0	Hydrophobic	false
N9	O	SER- 214	2.93	158.49	H-Bond (Ligand Donor)	false
C22	CB	TRP- 215	4.46	0	Hydrophobic	false
C19	CD2	TRP- 215	3.81	0	Hydrophobic	false
C20	CE3	TRP- 215	3.29	0	Hydrophobic	false
C28	CG	GLU- 217	3.77	0	Hydrophobic	false
C29	CB	GLU- 217	3.56	0	Hydrophobic	false
N3	O	GLY- 219	3.15	162.17	H-Bond (Ligand Donor)	false
O32	NH1	ARG- 221	2.97	121.46	H-Bond (Protein Donor)	false
O32	CZ	ARG- 221	3.46	0	Ionic (Protein Cationic)	false