scPDB - 3svj entry

Protein Data Bank Entry:

PDB ID : 3svj

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2011-07-12

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:	DEF_STRR6
AC:	Q8DP79
Organism:	Streptococcus pneumoniae
Reign:	Bacteria
TaxID:	171101
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.930
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.804	347.625

% Hydrophobic	% Polar
57.28	42.72
According to VolSite

Ligand :

HET Code:	4LI
Formula:	C27H32ClN9O2S
Molecular weight:	582.120 g/mol
DrugBank ID:	-
Buried Surface Area:	46.45 %
Polar Surface area:	143.92 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
23.2456	-7.9846	6.2782

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
CL40	CG	GLN- 57	3.85	0	Hydrophobic	false
C7	CG	GLN- 57	4.13	0	Hydrophobic	false
O38	N	VAL- 71	2.94	176.88	H-Bond (Protein Donor)	false
CL40	CG1	VAL- 71	3.65	0	Hydrophobic	false
C21	CG1	VAL- 71	4.02	0	Hydrophobic	false
C24	CG2	VAL- 71	3.66	0	Hydrophobic	false
CL40	CG	PRO- 90	4.33	0	Hydrophobic	false
C23	CD1	LEU- 124	4.33	0	Hydrophobic	false
C25	CD1	LEU- 124	4.04	0	Hydrophobic	false
N35	O	GLU- 126	2.6	165.28	H-Bond (Ligand Donor)	false
C3	CB	GLU- 126	3.5	0	Hydrophobic	false
N34	O	GLY- 127	2.79	158.55	H-Bond (Ligand Donor)	false
C23	CG	GLU- 128	3.8	0	Hydrophobic	false
N30	N	GLY- 129	3.25	163.43	H-Bond (Protein Donor)	false
N36	O	GLY- 129	2.85	142.63	H-Bond (Ligand Donor)	false
S39	CG2	ILE- 169	4.4	0	Hydrophobic	false
S39	CG2	VAL- 170	4.25	0	Hydrophobic	false
S39	CB	HIS- 173	3.66	0	Hydrophobic	false