scPDB - 2h29 entry

Protein Data Bank Entry:

PDB ID : 2h29

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-05-18

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_STAAC
AC:	Q5HFG7
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93062
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.339
Number of residues:	52
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.482	1002.375

% Hydrophobic	% Polar
38.05	61.95
According to VolSite

Ligand :

HET Code:	DND
Formula:	C21H24N6O15P2
Molecular weight:	662.394 g/mol
DrugBank ID:	DB04099
Buried Surface Area:	75.4 %
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
29.6574	30.7833	10.1956

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
C4B	CE1	TYR- 7	3.73	0	Hydrophobic	false
O4B	OH	TYR- 7	2.84	138.42	H-Bond (Protein Donor)	false
O14	N	GLN- 10	2.99	143.49	H-Bond (Protein Donor)	false
O12	OG	SER- 42	2.53	155.61	H-Bond (Protein Donor)	false
C2D	CB	SER- 42	4.19	0	Hydrophobic	false
C3N	CG	PRO- 43	3.7	0	Hydrophobic	false
C4N	CB	PRO- 43	3.66	0	Hydrophobic	false
C4N	CD1	LEU- 44	4	0	Hydrophobic	false
O11	NZ	LYS- 45	2.72	163.06	H-Bond (Protein Donor)	false
O11	NZ	LYS- 45	2.72	0	Ionic (Protein Cationic)	false
O13	NZ	LYS- 45	2.94	0	Ionic (Protein Cationic)	false
O7N	N	THR- 85	2.95	166.54	H-Bond (Protein Donor)	false
C4D	CE2	PHE- 103	4.24	0	Hydrophobic	false
O3B	N	GLY- 106	3.23	151.01	H-Bond (Protein Donor)	false
O2B	N	GLY- 106	3.09	124.7	H-Bond (Protein Donor)	false
C5D	CG	GLN- 109	4.26	0	Hydrophobic	false
C3B	CG	GLN- 109	4.18	0	Hydrophobic	false
C4D	CH2	TRP- 116	4.36	0	Hydrophobic	false
C3N	CB	TRP- 116	4.27	0	Hydrophobic	false
DuAr	DuAr	TRP- 116	3.72	0	Aromatic Face/Face	false
O8N	N	TYR- 117	2.75	164.07	H-Bond (Protein Donor)	false
N6A	O	VAL- 152	2.8	152.26	H-Bond (Ligand Donor)	false
N6A	O	ILE- 154	2.99	162.69	H-Bond (Ligand Donor)	false
O3D	O	HOH- 1005	2.61	170.91	H-Bond (Ligand Donor)	false
O2D	O	HOH- 1009	2.64	153.55	H-Bond (Ligand Donor)	false
N1A	O	HOH- 1012	2.95	179.97	H-Bond (Protein Donor)	false
O11	O	HOH- 1046	2.73	140.58	H-Bond (Protein Donor)	false