scPDB - 4bfy entry

Protein Data Bank Entry:

PDB ID : 4bfy

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-03-22

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
B	100 %

Ligand binding site composition:

B-Factor:	27.947
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	894.375

% Hydrophobic	% Polar
50.57	49.43
According to VolSite

Ligand :

HET Code:	ZVY
Formula:	C25H24N4O3
Molecular weight:	428.483 g/mol
DrugBank ID:	-
Buried Surface Area:	58.31 %
Polar Surface area:	93.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-68.8316	-9.00084	21.2743

Binding mode :

What is Poseview ?

2D View
3D View

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
CAE	CD1	LEU- 132	3.79	0	Hydrophobic	false
CAH	CG	LYS- 147	4.11	0	Hydrophobic	false
CAR	CD	LYS- 147	4.16	0	Hydrophobic	false
OAB	OH	TYR- 182	2.71	173.47	H-Bond (Protein Donor)	false
OAW	OH	TYR- 182	3.5	120.02	H-Bond (Protein Donor)	false
CAR	CE2	TYR- 182	4.27	0	Hydrophobic	false
CAF	CD1	LEU- 203	3.76	0	Hydrophobic	false
CAT	CZ	TYR- 235	3.85	0	Hydrophobic	false
OAC	CZ	ARG- 238	3.7	0	Ionic (Protein Cationic)	false
OAC	NH2	ARG- 238	2.74	161.54	H-Bond (Protein Donor)	false
CAT	CD2	PHE- 239	3.4	0	Hydrophobic	false
CAT	SD	MET- 242	4.15	0	Hydrophobic	false
CAT	CZ	PHE- 247	4.29	0	Hydrophobic	false
CBB	CG2	ILE- 272	3.64	0	Hydrophobic	false
CBD	CG2	ILE- 272	4.04	0	Hydrophobic	false
CAN	CD1	ILE- 272	3.84	0	Hydrophobic	false
CAJ	CG1	ILE- 276	4.4	0	Hydrophobic	false
CAS	CG2	ILE- 276	4.48	0	Hydrophobic	false
CAY	CD1	ILE- 276	4	0	Hydrophobic	false
CAM	CD1	ILE- 276	3.24	0	Hydrophobic	false
OAC	O	HOH- 2072	2.83	120.36	H-Bond (Protein Donor)	false