scPDB - 3fv4 entry

Protein Data Bank Entry:

PDB ID : 3fv4

Resolution :1.560 Å

Experimental Method : X-ray

Deposition Date : 2009-01-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thermolysin
ID:	THER_BACTH
AC:	P00800
Organism:	Bacillus thermoproteolyticus
Reign:	Bacteria
TaxID:	1427
EC Number:	3.4.24.27

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	9.436
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.053	246.375

% Hydrophobic	% Polar
45.21	54.79
According to VolSite

Ligand :

HET Code:	1U4
Formula:	C24H30N3O7P
Molecular weight:	503.485 g/mol
DrugBank ID:	-
Buried Surface Area:	53.26 %
Polar Surface area:	169.52 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-11.1505	40.2303	5.67283

Binding mode :

What is Poseview ?

2D View
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
N18	OD1	ASN- 112	3.17	157.54	H-Bond (Ligand Donor)	false
O34	ND2	ASN- 112	2.97	165.82	H-Bond (Protein Donor)	false
N14	O	ALA- 113	2.81	131.05	H-Bond (Ligand Donor)	false
C61	CB	PHE- 114	4.42	0	Hydrophobic	false
C26	CZ	PHE- 130	3.63	0	Hydrophobic	false
C22	CE2	PHE- 130	4.15	0	Hydrophobic	false
C42	CD2	LEU- 133	4.17	0	Hydrophobic	false
C50	CG1	VAL- 139	4.15	0	Hydrophobic	false
C44	CG2	VAL- 139	3.85	0	Hydrophobic	false
C46	CG2	VAL- 139	3.63	0	Hydrophobic	false
C50	CB	HIS- 142	4.2	0	Hydrophobic	false
O54	OE1	GLU- 143	2.59	160.64	H-Bond (Protein Donor)	false
N14	OE2	GLU- 143	3.32	125.11	H-Bond (Ligand Donor)	false
C7	CE2	TYR- 157	4.11	0	Hydrophobic	false
N11	OH	TYR- 157	3.41	127.58	H-Bond (Ligand Donor)	false
C46	CG2	ILE- 188	3.3	0	Hydrophobic	false
C22	CD1	LEU- 202	4.18	0	Hydrophobic	false
C26	CD2	LEU- 202	3.78	0	Hydrophobic	false
C44	CD2	LEU- 202	3.31	0	Hydrophobic	false
O17	NH2	ARG- 203	2.98	139.69	H-Bond (Protein Donor)	false
O17	NH1	ARG- 203	2.9	144.03	H-Bond (Protein Donor)	false
O55	NE2	HIS- 231	2.86	176.38	H-Bond (Protein Donor)	false
O55	ZN	ZN- 321	1.99	0	Metal Acceptor	false