scPDB - 1n2i entry

Protein Data Bank Entry:

PDB ID : 1n2i

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2002-10-22

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_MYCTU
AC:	P9WIL5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	6.3.2.1

Chains:

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

Ligand binding site composition:

B-Factor:	21.005
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.617	1120.500

% Hydrophobic	% Polar
38.25	61.75
According to VolSite

Ligand :

HET Code:	PAJ
Formula:	C16H23N5O10P
Molecular weight:	476.355 g/mol
DrugBank ID:	DB02694
Buried Surface Area:	75.45 %
Polar Surface area:	245.23 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
18.1367	14.8485	75.7341

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
C14	CB	PRO- 38	3.85	0	Hydrophobic	false
C15	CB	PRO- 38	4.23	0	Hydrophobic	false
C5'	CB	THR- 39	4.17	0	Hydrophobic	false
O2P	N	MET- 40	2.82	158.12	H-Bond (Protein Donor)	false
C12	CG	MET- 40	4.09	0	Hydrophobic	false
C14	CG	MET- 40	3.99	0	Hydrophobic	false
C1'	CD2	LEU- 50	3.98	0	Hydrophobic	false
C4'	CD2	LEU- 50	3.87	0	Hydrophobic	false
O13	NE2	GLN- 72	2.94	159.03	H-Bond (Protein Donor)	false
O14	OE1	GLN- 72	2.7	170.52	H-Bond (Ligand Donor)	false
C16	CG1	VAL- 139	4.44	0	Hydrophobic	false
C16	CG1	VAL- 142	3.62	0	Hydrophobic	false
C15	CG2	VAL- 143	4.08	0	Hydrophobic	false
C16	CG2	VAL- 143	4.25	0	Hydrophobic	false
C15	CE2	PHE- 157	3.61	0	Hydrophobic	false
O3'	N	GLY- 158	2.87	164.27	H-Bond (Protein Donor)	false
O2'	N	GLY- 158	3.44	123.96	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 161	2.55	153.96	H-Bond (Ligand Donor)	false
O11	NE2	GLN- 164	2.99	158.62	H-Bond (Protein Donor)	false
O13	OE1	GLN- 164	2.66	133.91	H-Bond (Ligand Donor)	false
N6	O	VAL- 187	3.09	168.86	H-Bond (Ligand Donor)	false
N1	N	VAL- 187	2.87	174.84	H-Bond (Protein Donor)	false
N6	O	MET- 195	2.96	159.76	H-Bond (Ligand Donor)	false
O3'	O	HOH- 1030	2.67	157.53	H-Bond (Ligand Donor)	false