scPDB - 4de5 entry

Protein Data Bank Entry:

PDB ID : 4de5

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2012-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate synthetase
ID:	PANC_MYCTO
AC:	P9WIL4
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83331
EC Number:	6.3.2.1

Chains:

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

Ligand binding site composition:

B-Factor:	23.055
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.662	438.750

% Hydrophobic	% Polar
45.38	54.62
According to VolSite

Ligand :

HET Code:	0JD
Formula:	C9H7O4
Molecular weight:	179.149 g/mol
DrugBank ID:	-
Buried Surface Area:	58.6 %
Polar Surface area:	58.59 Å2

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

Mass center Coordinates

X	Y	Z
1.71008	-10.3358	31.9653

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
CAD	CB	PRO- 38	3.89	0	Hydrophobic	false
OAB	N	MET- 40	2.66	169.04	H-Bond (Protein Donor)	false
CAM	CE	MET- 40	3.84	0	Hydrophobic	false
CAF	CG	MET- 40	3.77	0	Hydrophobic	false
OAA	NE2	HIS- 47	2.99	142.2	H-Bond (Protein Donor)	false
OAB	NE2	HIS- 47	3.22	147.6	H-Bond (Protein Donor)	false
CAE	CG1	VAL- 139	4.22	0	Hydrophobic	false
CAD	CG1	VAL- 142	3.97	0	Hydrophobic	false
CAC	CG2	VAL- 143	3.54	0	Hydrophobic	false
OAH	NE2	GLN- 164	2.81	154.83	H-Bond (Protein Donor)	false