scPDB - 2ntj entry

Protein Data Bank Entry:

PDB ID : 2ntj

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-11-07

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:	INHA_MYCTU
AC:	P9WGR1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	1.3.1.9

Chains:

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

Ligand binding site composition:

B-Factor:	35.595
Number of residues:	56
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.263	1100.250

% Hydrophobic	% Polar
55.83	44.17
According to VolSite

Ligand :

HET Code:	P1H
Formula:	C30H36N8O15P2
Molecular weight:	810.599 g/mol
DrugBank ID:	-
Buried Surface Area:	67.9 %
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
21.7754	-24.0571	13.16

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	3.63	0	Hydrophobic	false
C4	CB	ILE- 16	4.32	0	Hydrophobic	false
O9	N	ILE- 21	2.76	178.12	H-Bond (Protein Donor)	false
N4	CE1	PHE- 41	2.77	164.41	Weak HBond LIG	false
N4	OD1	ASP- 64	3.86	0	Ionic (Ligand Cationic)	false
N3	OD1	ASP- 64	3.62	0	Ionic (Ligand Cationic)	false
C5	CG1	ILE- 95	3.97	0	Hydrophobic	false
O4	N	GLY- 96	3.36	162.7	H-Bond (Protein Donor)	false
C15	CB	MET- 147	3.68	0	Hydrophobic	false
C12	CB	MET- 147	3.77	0	Hydrophobic	false
C19	CB	PHE- 149	4.42	0	Hydrophobic	false
C24	CB	PHE- 149	3.44	0	Hydrophobic	false
C29	CE1	PHE- 149	4.31	0	Hydrophobic	false
C20	CB	PHE- 149	3.42	0	Hydrophobic	false
C29	SD	MET- 155	4.02	0	Hydrophobic	false
C30	CE2	TYR- 158	3.49	0	Hydrophobic	false
O12	NZ	LYS- 165	3.07	142.64	H-Bond (Protein Donor)	false
O13	NZ	LYS- 165	2.86	142.12	H-Bond (Protein Donor)	false
C20	CB	ALA- 191	4.05	0	Hydrophobic	false
C24	CB	PRO- 193	4.27	0	Hydrophobic	false
N7	O	ILE- 194	3.04	148.24	H-Bond (Ligand Donor)	false
O14	N	ILE- 194	2.7	157.12	H-Bond (Protein Donor)	false
O8	OG1	THR- 196	2.92	167.31	H-Bond (Protein Donor)	false
C30	CD1	LEU- 218	3.68	0	Hydrophobic	false
C28	CZ3	TRP- 222	4.29	0	Hydrophobic	false
O9	O	HOH- 402	2.9	180	H-Bond (Protein Donor)	false