scPDB - 1d0v entry

Protein Data Bank Entry:

PDB ID : 1d0v

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1999-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
ID:	COBT_SALTY
AC:	Q05603
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	2.4.2.21

Chains:

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

Ligand binding site composition:

B-Factor:	14.890
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.947	418.500

% Hydrophobic	% Polar
54.03	45.97
According to VolSite

Ligand :

HET Code:	RBZ
Formula:	C14H17N2O7P
Molecular weight:	356.268 g/mol
DrugBank ID:	DB02030
Buried Surface Area:	63.73 %
Polar Surface area:	149.74 Å2

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

Mass center Coordinates

X	Y	Z
58.265	40.7255	10.7035

Binding mode :

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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
C9	CB	SER- 80	3.73	0	Hydrophobic	false
C8	CG1	VAL- 84	3.76	0	Hydrophobic	false
C4	CG	GLN- 88	3.79	0	Hydrophobic	false
O2'	OE1	GLU- 174	2.63	165.27	H-Bond (Ligand Donor)	false
O3'	N	GLY- 176	2.89	166.3	H-Bond (Protein Donor)	false
C3'	CE	MET- 177	4.35	0	Hydrophobic	false
C7	CE	MET- 177	4.03	0	Hydrophobic	false
C9	SD	MET- 177	4.18	0	Hydrophobic	false
O3P	N	ALA- 178	2.71	163.8	H-Bond (Protein Donor)	false
O1P	N	THR- 180	3.04	159.36	H-Bond (Protein Donor)	false
O1P	OG1	THR- 180	2.67	165.05	H-Bond (Protein Donor)	false
C5'	CG2	THR- 180	3.54	0	Hydrophobic	false
C7	CB	ALA- 203	4.2	0	Hydrophobic	false
C9	CB	ALA- 203	4.5	0	Hydrophobic	false
O2P	N	ALA- 203	2.86	168.46	H-Bond (Protein Donor)	false
O5'	N	ALA- 203	3.4	128.2	H-Bond (Protein Donor)	false
C7A	CD1	LEU- 315	4.41	0	Hydrophobic	false
C4	CD1	LEU- 315	4.41	0	Hydrophobic	false
O2P	O	HOH- 490	2.81	170.75	H-Bond (Protein Donor)	false