scPDB - 3dla entry

Protein Data Bank Entry:

PDB ID : 3dla

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2008-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamine-dependent NAD(+) synthetase
ID:	NADE_MYCTU
AC:	P9WJJ3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	6.3.5.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	41 %
D	59 %

Ligand binding site composition:

B-Factor:	6.079
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.529	688.500

% Hydrophobic	% Polar
41.67	58.33
According to VolSite

Ligand :

HET Code:	NXX
Formula:	C21H24N6O15P2
Molecular weight:	662.394 g/mol
DrugBank ID:	-
Buried Surface Area:	55.98 %
Polar Surface area:	340.58 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
154.125	92.6459	46.3542

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
N1A	NE	ARG- 354	3.09	152.6	H-Bond (Protein Donor)	false
N1A	NH2	ARG- 354	3.06	148.71	H-Bond (Protein Donor)	false
C5M	CG1	VAL- 452	4.47	0	Hydrophobic	false
O2M	OE2	GLU- 455	3.05	142	H-Bond (Ligand Donor)	false
O3M	OE2	GLU- 455	2.96	140.21	H-Bond (Ligand Donor)	false
O3A	ND2	ASN- 456	3.41	158.7	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 471	3.4	176.59	H-Bond (Protein Donor)	false
O2P	O	GLY- 475	2.66	127.12	H-Bond (Ligand Donor)	false
C1B	CG2	ILE- 476	4.05	0	Hydrophobic	false
C2M	CH2	TRP- 490	4.42	0	Hydrophobic	false
C5N	CB	THR- 492	4.37	0	Hydrophobic	false
O2A	N	TYR- 493	2.74	149.63	H-Bond (Protein Donor)	false
C5N	CB	ASP- 497	4.5	0	Hydrophobic	false
C1B	CZ	PHE- 634	4.07	0	Hydrophobic	false
C5B	CZ	PHE- 634	4.08	0	Hydrophobic	false
DuAr	DuAr	PHE- 634	3.72	0	Aromatic Face/Face	false
O1N	NZ	LYS- 635	2.59	149.07	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 635	2.93	127.89	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 635	2.59	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 635	2.93	0	Ionic (Protein Cationic)	false
N6A	O	SER- 661	3.21	132.46	H-Bond (Ligand Donor)	false