scPDB - 4ybr entry

Protein Data Bank Entry:

PDB ID : 4ybr

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2015-02-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable nicotinate-nucleotide adenylyltransferase
ID:	NADD_MYCTU
AC:	P9WJJ5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.7.7.18

Chains:

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

Ligand binding site composition:

B-Factor:	22.490
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.342	465.750

% Hydrophobic	% Polar
38.41	61.59
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.71 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-16.5746	19.9012	-18.603

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
N6A	O	GLY- 10	2.93	160.82	H-Bond (Ligand Donor)	false
O1N	N	THR- 12	2.96	156.82	H-Bond (Protein Donor)	false
O1X	NE2	HIS- 17	2.84	170	H-Bond (Protein Donor)	false
O2X	NE2	HIS- 20	2.64	165.75	H-Bond (Protein Donor)	false
O2D	OG	SER- 41	2.81	174.05	H-Bond (Protein Donor)	false
C2D	CB	SER- 41	4.03	0	Hydrophobic	false
O7N	OG1	THR- 86	3.26	153.93	H-Bond (Protein Donor)	false
O7N	N	THR- 86	3.23	171.55	H-Bond (Protein Donor)	false
C4D	CB	THR- 106	3.85	0	Hydrophobic	false
C5B	CB	ASP- 109	4.1	0	Hydrophobic	false
C5B	CB	ALA- 110	4.4	0	Hydrophobic	false
C5D	CB	ALA- 110	3.62	0	Hydrophobic	false
C5N	CB	SER- 113	4.39	0	Hydrophobic	false
C3N	CG1	ILE- 114	3.41	0	Hydrophobic	false
O1X	N	SER- 168	2.93	153.24	H-Bond (Protein Donor)	false
O3D	O	HOH- 416	2.66	156.3	H-Bond (Ligand Donor)	false
O2D	O	HOH- 493	3.32	168.24	H-Bond (Ligand Donor)	false