scPDB - 1uma entry

Protein Data Bank Entry:

PDB ID : 1uma

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1996-03-26

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:	34.772
Number of residues:	20
Including
Standard Amino Acids:	18
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.810	604.125

% Hydrophobic	% Polar
41.34	58.66
According to VolSite

Ligand :

HET Code:	IN2
Formula:	C8H18N4O3
Molecular weight:	218.254 g/mol
DrugBank ID:	-
Buried Surface Area:	48.45 %
Polar Surface area:	103.35 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
19.9031	-15.5589	22.5777

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
C5	CZ	TYR- 60	4.32	0	Hydrophobic	false
C3	CZ	TYR- 60	3.62	0	Hydrophobic	false
C3	CD1	LEU- 99	4.29	0	Hydrophobic	false
O8	O	HOH- 730	3.35	172.57	H-Bond (Protein Donor)	false