scPDB - 1kqo entry

Protein Data Bank Entry:

PDB ID : 1kqo

Resolution :2.500 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:	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
ID:	NMNA1_HUMAN
AC:	Q9HAN9
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.7.1

Chains:

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

Ligand binding site composition:

B-Factor:	53.027
Number of residues:	52
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.092	961.875

% Hydrophobic	% Polar
49.12	50.88
According to VolSite

Ligand :

HET Code:	DND
Formula:	C21H24N6O15P2
Molecular weight:	662.394 g/mol
DrugBank ID:	DB04099
Buried Surface Area:	66.79 %
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
45.0672	44.2494	2.52739

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
O11	OG	SER- 16	2.63	162.09	H-Bond (Protein Donor)	false
O3P	N	SER- 16	2.8	164.4	H-Bond (Protein Donor)	false
O5D	N	SER- 16	3.46	130.64	H-Bond (Protein Donor)	false
O13	N	PHE- 17	2.89	151.44	H-Bond (Protein Donor)	false
C5B	CZ	PHE- 17	3.99	0	Hydrophobic	false
C4B	CD2	LEU- 27	4.39	0	Hydrophobic	false
C1B	CD2	LEU- 27	3.7	0	Hydrophobic	false
C2D	CG2	VAL- 51	4.39	0	Hydrophobic	false
C5D	CZ	TYR- 55	4.47	0	Hydrophobic	false
C2D	CZ	TYR- 55	3.83	0	Hydrophobic	false
O11	NZ	LYS- 57	2.81	174.87	H-Bond (Protein Donor)	false
O11	NZ	LYS- 57	2.81	0	Ionic (Protein Cationic)	false
O2D	NE1	TRP- 92	3.22	150.64	H-Bond (Protein Donor)	false
O7N	N	THR- 95	2.55	156.35	H-Bond (Protein Donor)	false
O3B	N	GLY- 156	3.29	132.34	H-Bond (Protein Donor)	false
O2B	N	GLY- 156	3.14	128.96	H-Bond (Protein Donor)	false
C2B	CB	ASP- 158	4.4	0	Hydrophobic	false
C3B	CB	LEU- 159	4.42	0	Hydrophobic	false
C4D	CD1	LEU- 159	3.85	0	Hydrophobic	false
O2B	N	LEU- 159	3.46	160.23	H-Bond (Protein Donor)	false
C5N	CG	LEU- 168	3.69	0	Hydrophobic	false
DuAr	DuAr	TRP- 169	3.56	0	Aromatic Face/Face	false
N1A	OE1	GLU- 215	3.3	147.94	H-Bond (Ligand Donor)	false
C5N	CG	PRO- 269	4.05	0	Hydrophobic	false
C4N	CB	PRO- 269	4.02	0	Hydrophobic	false
O13	O	HOH- 404	2.56	179.98	H-Bond (Protein Donor)	false
O3D	O	HOH- 406	2.63	145.6	H-Bond (Ligand Donor)	false
O2D	O	HOH- 416	2.71	137.47	H-Bond (Ligand Donor)	false
O8N	O	HOH- 435	2.54	157.75	H-Bond (Protein Donor)	false