scPDB - 3fgd entry

Protein Data Bank Entry:

PDB ID : 3fgd

Resolution :1.330 Å

Experimental Method : X-ray

Deposition Date : 2008-12-05

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:	9.936
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.078	334.125

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	BYA
Formula:	C10H10NO3
Molecular weight:	192.191 g/mol
DrugBank ID:	-
Buried Surface Area:	67.61 %
Polar Surface area:	69.23 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-9.56343	38.8727	3.11779

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
N6	OD1	ASN- 112	2.82	138.42	H-Bond (Ligand Donor)	false
C11	CZ	PHE- 130	3.49	0	Hydrophobic	false
C11	CD2	LEU- 133	3.54	0	Hydrophobic	false
C12	CG2	VAL- 139	3.45	0	Hydrophobic	false
O1	OE2	GLU- 143	2.69	141.83	H-Bond (Protein Donor)	false
C13	CG2	ILE- 188	3.74	0	Hydrophobic	false
C10	CD2	LEU- 202	3.38	0	Hydrophobic	false
O8	NH2	ARG- 203	2.96	150.98	H-Bond (Protein Donor)	false
O8	NH1	ARG- 203	3.08	143.59	H-Bond (Protein Donor)	false
O3	NE2	HIS- 231	2.73	178.41	H-Bond (Protein Donor)	false
O3	ZN	ZN- 321	1.97	0	Metal Acceptor	false
O1	ZN	ZN- 321	2.63	0	Metal Acceptor	false