scPDB - 1ih8 entry

Protein Data Bank Entry:

PDB ID : 1ih8

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2001-04-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NH(3)-dependent NAD(+) synthetase
ID:	NADE_BACSU
AC:	P08164
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	6.3.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	10.792
Number of residues:	46
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	6
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.730	857.250

% Hydrophobic	% Polar
42.91	57.09
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	67.99 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.159	60.2652	48.8356

Binding mode :

What is Poseview ?

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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
O2'	O	GLY- 44	2.68	157.61	H-Bond (Ligand Donor)	false
O2B	OG	SER- 46	2.81	155.58	H-Bond (Protein Donor)	false
C2'	CB	SER- 46	4.23	0	Hydrophobic	false
O3G	N	GLN- 49	2.94	138.81	H-Bond (Protein Donor)	false
O3B	N	ASP- 50	3.21	146.04	H-Bond (Protein Donor)	false
C3A	CB	ASP- 50	3.74	0	Hydrophobic	false
O1B	N	SER- 51	3.12	150.89	H-Bond (Protein Donor)	false
O1B	OG	SER- 51	3.2	154.24	H-Bond (Protein Donor)	false
C2'	CB	SER- 51	3.95	0	Hydrophobic	false
N1	NH1	ARG- 78	3.1	135.43	H-Bond (Protein Donor)	false
N1	N	LEU- 79	3.21	141.36	H-Bond (Protein Donor)	false
N6	OE1	GLN- 84	2.83	140.03	H-Bond (Ligand Donor)	false
C3'	CG2	THR- 157	4.29	0	Hydrophobic	false
C5'	CB	ASP- 173	3.78	0	Hydrophobic	false
O2G	NZ	LYS- 186	2.88	150.47	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 186	2.88	0	Ionic (Protein Cationic)	false
O1G	N	THR- 208	3.14	156.68	H-Bond (Protein Donor)	false
O1G	MG	MG- 4002	2.02	0	Metal Acceptor	false
O2B	MG	MG- 4002	1.92	0	Metal Acceptor	false
O1A	MG	MG- 4002	1.94	0	Metal Acceptor	false
O2A	MG	MG- 4003	2.27	0	Metal Acceptor	false