scPDB - 1k4m entry

Protein Data Bank Entry:

PDB ID : 1k4m

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2001-10-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nicotinate-nucleotide adenylyltransferase
ID:	NADD_ECOLI
AC:	P0A752
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.7.7.18

Chains:

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

Ligand binding site composition:

B-Factor:	29.683
Number of residues:	52
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.429	988.875

% Hydrophobic	% Polar
33.79	66.21
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.87 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
31.0412	53.6749	35.6669

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	CZ	PHE- 8	3.76	0	Hydrophobic	false
O1A	N	THR- 11	2.79	144.69	H-Bond (Protein Donor)	false
O1A	N	PHE- 12	3.02	168.18	H-Bond (Protein Donor)	false
C5B	CE2	PHE- 12	3.91	0	Hydrophobic	false
O2D	OD1	ASN- 40	2.95	153.19	H-Bond (Ligand Donor)	false
O1N	NE2	HIS- 45	2.94	166.07	H-Bond (Protein Donor)	false
C5N	CB	HIS- 45	4.09	0	Hydrophobic	false
O2A	CZ	ARG- 46	3.92	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 46	3.62	0	Ionic (Protein Cationic)	false
O1N	NH2	ARG- 46	2.89	161.28	H-Bond (Protein Donor)	false
O1N	NE	ARG- 46	3.45	136.5	H-Bond (Protein Donor)	false
O7N	N	THR- 85	3.07	151.41	H-Bond (Protein Donor)	false
C4D	CZ	PHE- 104	4.29	0	Hydrophobic	false
O3B	N	GLY- 107	3.04	142.84	H-Bond (Protein Donor)	false
O2B	N	GLY- 107	3.13	131.31	H-Bond (Protein Donor)	false
O2B	OD1	ASP- 109	2.59	143.81	H-Bond (Ligand Donor)	false
O2B	OG	SER- 110	2.92	165	H-Bond (Protein Donor)	false
C4D	CH2	TRP- 117	4.1	0	Hydrophobic	false
C3N	CB	TRP- 117	3.95	0	Hydrophobic	false
DuAr	DuAr	TRP- 117	3.68	0	Aromatic Face/Face	false
N6A	O	PHE- 177	3.16	153.64	H-Bond (Ligand Donor)	false
N6A	O	ILE- 179	3.02	147.66	H-Bond (Ligand Donor)	false
N1A	O	HOH- 617	2.78	151.94	H-Bond (Protein Donor)	false
O3D	O	HOH- 637	2.67	142.82	H-Bond (Ligand Donor)	false
O3D	O	HOH- 676	3.45	131.64	H-Bond (Protein Donor)	false
O7N	O	HOH- 680	2.84	141.94	H-Bond (Protein Donor)	false