scPDB - 3q1f entry

Protein Data Bank Entry:

PDB ID : 3q1f

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2010-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-lactamase
ID:	Q9L5C8_ECOLX
AC:	Q9L5C8
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	5.741
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.490	367.875

% Hydrophobic	% Polar
43.12	56.88
According to VolSite

Ligand :

HET Code:	YPP
Formula:	C23H28N5O8S
Molecular weight:	534.562 g/mol
DrugBank ID:	-
Buried Surface Area:	49.26 %
Polar Surface area:	220.98 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
25.8855	-16.1728	11.5808

Binding mode :

What is Poseview ?

2D View
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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
OXT	N	GLY- 70	2.83	130.99	H-Bond (Protein Donor)	false
O	NZ	LYS- 73	2.66	154.18	H-Bond (Protein Donor)	false
O	NZ	LYS- 73	2.66	0	Ionic (Protein Cationic)	false
OAQ	ND2	ASN- 104	3.07	166.89	H-Bond (Protein Donor)	false
CAN	CE2	TYR- 105	3.5	0	Hydrophobic	false
SAI	CD2	TYR- 105	3.63	0	Hydrophobic	false
OAQ	ND2	ASN- 132	2.9	150.96	H-Bond (Protein Donor)	false
CBK	CG2	THR- 168	3.6	0	Hydrophobic	false
CBK	CG2	THR- 171	4.08	0	Hydrophobic	false
N	O	SER- 237	2.89	147.17	H-Bond (Ligand Donor)	false
OXT	N	SER- 237	2.86	172.26	H-Bond (Protein Donor)	false
CAT	CB	SER- 237	3.69	0	Hydrophobic	false