scPDB - 1kqp entry

Protein Data Bank Entry:

PDB ID : 1kqp

Resolution :1.030 Å

Experimental Method : X-ray

Deposition Date : 2002-01-07

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	15 %
B	85 %

Ligand binding site composition:

B-Factor:	12.784
Number of residues:	78
Including
Standard Amino Acids:	69
Non Standard Amino Acids:	2
Water Molecules:	7
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.647	975.375

% Hydrophobic	% Polar
34.60	65.40
According to VolSite

Ligand :

HET Code:	ADJ
Formula:	C31H42N11O21P3
Molecular weight:	997.648 g/mol
DrugBank ID:	-
Buried Surface Area:	64.07 %
Polar Surface area:	508.95 Å2

Number of
H-Bond Acceptors:	29
H-Bond Donors:	10
Rings:	8
Aromatic rings:	4
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
-2.11536	62.1516	28.1977

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
N1	OH	TYR- 32	2.69	169.08	H-Bond (Protein Donor)	false
O2S	O	GLY- 44	2.67	154.21	H-Bond (Ligand Donor)	false
C2S	CB	SER- 46	4.36	0	Hydrophobic	false
C2S	CB	SER- 51	3.82	0	Hydrophobic	false
N1X	NH1	ARG- 78	3.05	120.49	H-Bond (Protein Donor)	false
N1X	N	LEU- 79	3.15	142.57	H-Bond (Protein Donor)	false
N6X	OE1	GLN- 84	2.81	137.01	H-Bond (Ligand Donor)	false
O2B	ND2	ASN- 133	3.16	172.67	H-Bond (Protein Donor)	false
C5N	CB	ALA- 136	4.16	0	Hydrophobic	false
O1A	CZ	ARG- 137	3.75	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 137	2.77	150.59	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 144	4.48	0	Hydrophobic	false
C2'	CD2	LEU- 153	4.16	0	Hydrophobic	false
O3S	OG1	THR- 157	2.72	164.5	H-Bond (Protein Donor)	false
C2R	CE2	PHE- 167	4.28	0	Hydrophobic	false
C5N	CB	THR- 169	3.69	0	Hydrophobic	false
O2A	N	LYS- 170	2.86	166.82	H-Bond (Protein Donor)	false
C1'	CD	LYS- 170	4.45	0	Hydrophobic	false
C5S	CB	ASP- 173	3.67	0	Hydrophobic	false
O2'	OD2	ASP- 177	2.69	164.67	H-Bond (Ligand Donor)	false
C3N	CB	ALA- 209	3.45	0	Hydrophobic	false
C5N	CD1	LEU- 211	3.41	0	Hydrophobic	false
O2R	OE1	GLU- 223	2.63	139.73	H-Bond (Ligand Donor)	false
O2R	OE2	GLU- 223	3.28	147.94	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 257	3.47	0	Aromatic Face/Face	false
O2A	NZ	LYS- 258	2.94	0	Ionic (Protein Cationic)	false
O5R	NZ	LYS- 258	2.97	143.41	H-Bond (Protein Donor)	false
O3P	MG	MG- 5003	2.03	0	Metal Acceptor	false
O1P	MG	MG- 5004	2.12	0	Metal Acceptor	false