scPDB - 2gfk entry

Protein Data Bank Entry:

PDB ID : 2gfk

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Metallo-beta-lactamase L1 type 3
ID:	BLA1_STEMA
AC:	P52700
Organism:	Stenotrophomonas maltophilia
Reign:	Bacteria
TaxID:	40324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.807
Number of residues:	24
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.185	246.375

% Hydrophobic	% Polar
60.27	39.73
According to VolSite

Ligand :

HET Code:	VII
Formula:	C18H10O5
Molecular weight:	306.269 g/mol
DrugBank ID:	DB08702
Buried Surface Area:	52.74 %
Polar Surface area:	93.4 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
18.98	24.4605	1.33826

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
C16	CG1	VAL- 35	4.15	0	Hydrophobic	false
C14	CB	ALA- 119	4.48	0	Hydrophobic	false
C14	CB	ASP- 120	4.04	0	Hydrophobic	false
C13	CD1	ILE- 162	4.2	0	Hydrophobic	false
C15	CG2	ILE- 162	3.51	0	Hydrophobic	false
O20	OG	SER- 225	3.19	149.58	H-Bond (Protein Donor)	false
O21	OG	SER- 225	2.72	143.83	H-Bond (Protein Donor)	false
O22	ZN	ZN- 401	2.65	0	Metal Acceptor	false
O23	ZN	ZN- 401	1.93	0	Metal Acceptor	false
O23	ZN	ZN- 402	2.15	0	Metal Acceptor	false
DuAr	ZN	ZN- 402	3.77	36.54	Pi/Cation	false