scPDB - 2ntv entry

Protein Data Bank Entry:

PDB ID : 2ntv

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-11-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Enoyl-[acyl-carrier-protein] reductase [NADH]
ID:	Q9CBM1_MYCLE
AC:	Q9CBM1
Organism:	Mycobacterium leprae
Reign:	Bacteria
TaxID:	272631
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.797
Number of residues:	63
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.352	1188.000

% Hydrophobic	% Polar
54.55	45.45
According to VolSite

Ligand :

HET Code:	P1H
Formula:	C30H36N8O15P2
Molecular weight:	810.599 g/mol
DrugBank ID:	-
Buried Surface Area:	67.73 %
Polar Surface area:	372.86 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-7.15738	-4.57053	33.3259

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
C3	CG2	ILE- 16	3.67	0	Hydrophobic	false
C4	CB	ILE- 16	4.39	0	Hydrophobic	false
O9	N	ILE- 21	2.75	163.75	H-Bond (Protein Donor)	false
N3	OD1	ASP- 64	2.79	157.36	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 64	2.79	0	Ionic (Ligand Cationic)	false
C11	CB	SER- 94	4.23	0	Hydrophobic	false
O4	N	GLY- 96	3.47	159.04	H-Bond (Protein Donor)	false
C12	CB	MET- 147	3.54	0	Hydrophobic	false
C26	CG	PHE- 149	3.37	0	Hydrophobic	false
C29	CD1	PHE- 149	3.77	0	Hydrophobic	false
C20	CB	PHE- 149	3.48	0	Hydrophobic	false
C29	SD	MET- 155	3.35	0	Hydrophobic	false
C26	CE1	TYR- 158	3.55	0	Hydrophobic	false
C30	CE2	TYR- 158	3.7	0	Hydrophobic	false
O12	NZ	LYS- 165	2.81	131.06	H-Bond (Protein Donor)	false
O13	NZ	LYS- 165	2.82	143.31	H-Bond (Protein Donor)	false
C20	CB	ALA- 191	3.9	0	Hydrophobic	false
N7	O	ILE- 194	3.37	128.07	H-Bond (Ligand Donor)	false
C30	CD1	LEU- 218	3.97	0	Hydrophobic	false
C30	CZ3	TRP- 222	3.9	0	Hydrophobic	false
O9	O	HOH- 302	2.79	179.98	H-Bond (Protein Donor)	false
O12	O	HOH- 303	2.87	136.74	H-Bond (Ligand Donor)	false
O6	O	HOH- 345	2.67	179.99	H-Bond (Protein Donor)	false