scPDB - 3p70 entry

Protein Data Bank Entry:

PDB ID : 3p70

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2010-10-11

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
D	62 %
F	38 %

Ligand binding site composition:

B-Factor:	61.642
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.525	877.500

% Hydrophobic	% Polar
40.38	59.62
According to VolSite

Ligand :

HET Code:	ILE_PHE_GLU_PRO_PRO
Formula:	C30H43N5O7
Molecular weight:	585.692 g/mol
DrugBank ID:	-
Buried Surface Area:	41.11 %
Polar Surface area:	183.65 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
28.9478	35.1699	56.3665

Binding mode :

What is Poseview ?

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3D View

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
CB	CZ	PHE- 382	4.15	0	Hydrophobic	false
CD2	CB	GLN- 387	4.48	0	Hydrophobic	false
CZ	CB	LEU- 389	4.16	0	Hydrophobic	false
CG2	CZ2	TRP- 413	4.41	0	Hydrophobic	false
CB	CE2	TRP- 413	3.68	0	Hydrophobic	false
CG	CD2	TRP- 413	3.94	0	Hydrophobic	false
CE1	CG	ARG- 431	4.49	0	Hydrophobic	false
N	O	THR- 432	2.92	123.76	H-Bond (Ligand Donor)	false
CE1	CG2	THR- 432	3.84	0	Hydrophobic	false
OE1	N	TYR- 434	2.92	132.13	H-Bond (Protein Donor)	false
CB	CE2	TYR- 434	4	0	Hydrophobic	false
CG	CB	TYR- 434	3.82	0	Hydrophobic	false
CB	CD1	ILE- 441	4.43	0	Hydrophobic	false
CB	CG2	THR- 510	3.9	0	Hydrophobic	false
CB	CH2	TRP- 511	4.43	0	Hydrophobic	false
CG	CZ3	TRP- 511	3.69	0	Hydrophobic	false
CG	CG	GLU- 565	3.93	0	Hydrophobic	false