scPDB - 3af4 entry

Protein Data Bank Entry:

PDB ID : 3af4

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-02-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate kinase
ID:	COAA_MYCTU
AC:	P9WPA7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.7.1.33

Chains:

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

Ligand binding site composition:

B-Factor:	40.545
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.913	1032.750

% Hydrophobic	% Polar
47.71	52.29
According to VolSite

Ligand :

HET Code:	GCP
Formula:	C11H14N5O13P3
Molecular weight:	517.176 g/mol
DrugBank ID:	DB03725
Buried Surface Area:	53.36 %
Polar Surface area:	326.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
41.7157	30.6959	17.4671

Binding mode :

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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
O1A	N	ALA- 100	2.64	128.4	H-Bond (Protein Donor)	false
O1B	N	GLY- 102	2.98	151.05	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 103	3.26	152.26	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 103	3.03	138.6	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 103	3.26	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 103	3.92	0	Ionic (Protein Cationic)	false
C3B	CB	SER- 104	3.38	0	Hydrophobic	false
O2B	N	SER- 104	2.58	168.02	H-Bond (Protein Donor)	false
O2G	N	THR- 105	2.75	143.6	H-Bond (Protein Donor)	false
O2G	OG1	THR- 105	2.82	148.03	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 108	3.45	0	Ionic (Protein Cationic)	false
O3G	NH2	ARG- 108	2.63	163.74	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 108	3.42	125.48	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 238	2.84	148.68	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 238	2.97	140.53	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 238	3.32	0	Ionic (Protein Cationic)	false
O1G	O	HOH- 467	3.22	146.67	H-Bond (Protein Donor)	false