scPDB - 3sw8 entry

Protein Data Bank Entry:

PDB ID : 3sw8

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptide deformylase
ID:	Q939R9_STREE
AC:	Q939R9
Organism:	Streptococcus pneumoniae
Reign:	Bacteria
TaxID:	1313
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.861
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.018	496.125

% Hydrophobic	% Polar
55.78	44.22
According to VolSite

Ligand :

HET Code:	5LI
Formula:	C10H10Cl2N2O3
Molecular weight:	277.104 g/mol
DrugBank ID:	-
Buried Surface Area:	76.61 %
Polar Surface area:	69.64 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
27.2469	-4.48329	6.53041

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
O14	N	VAL- 71	2.9	166.73	H-Bond (Protein Donor)	false
CL17	CG2	VAL- 71	4.03	0	Hydrophobic	false
C6	CG2	VAL- 71	3.89	0	Hydrophobic	false
O15	NE2	GLN- 77	3.03	154.22	H-Bond (Protein Donor)	false
C3	CD1	LEU- 124	3.64	0	Hydrophobic	false
C1	CB	GLU- 128	4.19	0	Hydrophobic	false
CL16	CG	GLU- 128	4.3	0	Hydrophobic	false
C3	CG	GLU- 128	3.76	0	Hydrophobic	false
N11	O	GLY- 129	2.89	166.84	H-Bond (Ligand Donor)	false
O15	N	LEU- 131	2.76	164.53	H-Bond (Protein Donor)	false
CL16	CG2	ILE- 169	3.62	0	Hydrophobic	false
CL16	CG2	VAL- 170	3.94	0	Hydrophobic	false
CL17	CG1	VAL- 170	4.3	0	Hydrophobic	false
CL16	CB	HIS- 173	3.63	0	Hydrophobic	false
CL17	CB	HIS- 173	3.95	0	Hydrophobic	false
O13	OE1	GLU- 174	2.7	152.34	H-Bond (Protein Donor)	false