scPDB - 1nqw entry

Protein Data Bank Entry:

PDB ID : 1nqw

Resolution :2.200 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	64 %
B	36 %

Ligand binding site composition:

B-Factor:	16.306
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.838	756.000

% Hydrophobic	% Polar
49.11	50.89
According to VolSite

Ligand :

HET Code:	5YL
Formula:	C14H24N3O9P
Molecular weight:	409.329 g/mol
DrugBank ID:	-
Buried Surface Area:	71.96 %
Polar Surface area:	224.14 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	7
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
142.843	12.4998	146.048

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
C13	CZ	PHE- 22	3.57	0	Hydrophobic	false
C8	CD1	PHE- 22	3.83	0	Hydrophobic	false
O2	N	SER- 56	2.85	153.03	H-Bond (Protein Donor)	false
O2	OG	SER- 56	2.72	154.04	H-Bond (Protein Donor)	false
O9	N	TRP- 57	3.15	166.27	H-Bond (Protein Donor)	false
C10	CB	TRP- 57	3.67	0	Hydrophobic	false
O10	OE2	GLU- 58	3.44	134.28	H-Bond (Ligand Donor)	false
O10	OE1	GLU- 58	2.73	166.24	H-Bond (Ligand Donor)	false
O12	OE2	GLU- 58	2.61	168.98	H-Bond (Ligand Donor)	false
N3	O	VAL- 80	2.9	163.11	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 81	4.38	0	Hydrophobic	false
O4	N	ILE- 82	3.17	166.31	H-Bond (Protein Donor)	false
O3P	N	ALA- 85	2.84	165.02	H-Bond (Protein Donor)	false
O2P	OG1	THR- 86	2.53	172.34	H-Bond (Protein Donor)	false
O2P	N	THR- 86	2.97	147.99	H-Bond (Protein Donor)	false
C16	CB	HIS- 88	4.4	0	Hydrophobic	false
C14	CD1	ILE- 92	4.43	0	Hydrophobic	false
C9	CD1	ILE- 92	3.96	0	Hydrophobic	false
C12	CB	THR- 112	4.45	0	Hydrophobic	false
O11	O	PHE- 113	2.92	150.37	H-Bond (Ligand Donor)	false
O12	N	PHE- 113	2.97	159.41	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 127	3.72	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 127	3.53	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 127	2.82	167.65	H-Bond (Protein Donor)	false
O1P	NE	ARG- 127	2.7	179.32	H-Bond (Protein Donor)	false
O11	NZ	LYS- 135	2.81	150.85	H-Bond (Protein Donor)	false
C11	CG	GLU- 138	4.4	0	Hydrophobic	false
C12	CB	ALA- 139	4.35	0	Hydrophobic	false
C12	CB	SER- 142	4.06	0	Hydrophobic	false
O2	O	HOH- 1301	2.9	179.95	H-Bond (Protein Donor)	false
O2P	O	HOH- 1303	2.54	179.96	H-Bond (Protein Donor)	false
N7	O	HOH- 1319	3.12	126.85	H-Bond (Ligand Donor)	false