scPDB - 1nqv entry

Protein Data Bank Entry:

PDB ID : 1nqv

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2003-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6,7-dimethyl-8-ribityllumazine synthase
ID:	RISB_AQUAE
AC:	O66529
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	2.5.1.78

Chains:

Chain Name:	Percentage of Residues within binding site
A	66 %
B	34 %

Ligand binding site composition:

B-Factor:	15.511
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.864	749.250

% Hydrophobic	% Polar
52.25	47.75
According to VolSite

Ligand :

HET Code:	LMZ
Formula:	C9H14N4O7
Molecular weight:	290.230 g/mol
DrugBank ID:	DB04128
Buried Surface Area:	71.31 %
Polar Surface area:	180.58 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	7
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
141.932	13.4415	144.279

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
C8	CD1	PHE- 22	3.56	0	Hydrophobic	false
O2	N	SER- 56	2.86	150.37	H-Bond (Protein Donor)	false
O2	OG	SER- 56	2.82	151.19	H-Bond (Protein Donor)	false
O9	N	TRP- 57	3.12	169.54	H-Bond (Protein Donor)	false
C10	CB	TRP- 57	3.67	0	Hydrophobic	false
O10	OE2	GLU- 58	3.47	135.26	H-Bond (Ligand Donor)	false
O10	OE1	GLU- 58	2.68	167.67	H-Bond (Ligand Donor)	false
O12	OE2	GLU- 58	2.6	168.42	H-Bond (Ligand Donor)	false
N3	O	VAL- 80	2.8	166.67	H-Bond (Ligand Donor)	false
O4	N	ILE- 82	3.22	161.56	H-Bond (Protein Donor)	false
C9	CD1	ILE- 92	4.01	0	Hydrophobic	false
C12	CB	THR- 112	4.43	0	Hydrophobic	false
O11	O	PHE- 113	2.87	143.16	H-Bond (Ligand Donor)	false
C12	CB	PHE- 113	4.47	0	Hydrophobic	false
O12	N	PHE- 113	2.92	166.62	H-Bond (Protein Donor)	false
C12	CB	ALA- 139	4.4	0	Hydrophobic	false
C12	CB	SER- 142	4.05	0	Hydrophobic	false
O2	O	HOH- 1302	2.77	179.95	H-Bond (Protein Donor)	false