scPDB - 2zsd entry

Protein Data Bank Entry:

PDB ID : 2zsd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-09-05

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:	43.559
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.947	1080.000

% Hydrophobic	% Polar
49.06	50.94
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	61.95 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
45.0671	36.4055	29.2733

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
CAP	CG2	VAL- 99	4.13	0	Hydrophobic	false
O1A	N	ALA- 100	2.56	151.72	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 103	2.91	148.62	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 103	2.53	136.68	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 103	2.91	0	Ionic (Protein Cationic)	false
O4A	NZ	LYS- 103	2.53	0	Ionic (Protein Cationic)	false
O7A	OG	SER- 104	2.8	159.28	H-Bond (Protein Donor)	false
O8A	OG	SER- 104	3.16	126.76	H-Bond (Protein Donor)	false
C5B	CB	SER- 104	4.42	0	Hydrophobic	false
O7A	CZ	ARG- 108	3.49	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 108	3.93	0	Ionic (Protein Cationic)	false
O7A	NH1	ARG- 108	2.63	159.76	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 108	3.37	162.79	H-Bond (Protein Donor)	false
O5A	OD2	ASP- 129	3.16	163.72	H-Bond (Protein Donor)	false
CDP	CD1	LEU- 132	4.37	0	Hydrophobic	false
CEP	CD1	LEU- 132	4.48	0	Hydrophobic	false
CDP	CG	LYS- 147	4.49	0	Hydrophobic	false
CEP	CZ	TYR- 177	4.05	0	Hydrophobic	false
O5A	NE2	HIS- 179	3.16	156.96	H-Bond (Protein Donor)	false
CEP	CE1	TYR- 182	4.29	0	Hydrophobic	false
C6P	CZ	TYR- 182	4.32	0	Hydrophobic	false
CDP	CD1	LEU- 203	4.11	0	Hydrophobic	false
O1A	NH1	ARG- 238	3.38	136.4	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 238	2.92	164.53	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 238	3.59	0	Ionic (Protein Cationic)	false
S1P	CE1	PHE- 239	3.88	0	Hydrophobic	false
C1B	CE	MET- 242	4.38	0	Hydrophobic	false
S1P	CZ	PHE- 247	3.6	0	Hydrophobic	false
C2P	CZ	PHE- 254	3.24	0	Hydrophobic	false
S1P	CE2	PHE- 254	3.93	0	Hydrophobic	false
S1P	CE1	TYR- 257	4.37	0	Hydrophobic	false
C6P	CG2	ILE- 276	4.35	0	Hydrophobic	false
O5P	ND2	ASN- 277	3.39	154.24	H-Bond (Protein Donor)	false
O5A	O	HOH- 445	3.35	179.98	H-Bond (Protein Donor)	false