scPDB - 3qdl entry

Protein Data Bank Entry:

PDB ID : 3qdl

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-01-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxygen-insensitive NADPH nitroreductase
ID:	RDXA_HELPY
AC:	O25608
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	32 %
D	68 %

Ligand binding site composition:

B-Factor:	15.934
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.374	911.250

% Hydrophobic	% Polar
28.15	71.85
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	67.41 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
8.60368	4.16816	-31.3259

Binding mode :

What is Poseview ?

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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
O2P	CZ	ARG- 16	3.85	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 16	2.81	159.16	H-Bond (Protein Donor)	false
O1P	N	SER- 18	3.12	158.17	H-Bond (Protein Donor)	false
O2P	OG	SER- 18	2.97	154.71	H-Bond (Protein Donor)	false
C1'	CB	SER- 18	3.75	0	Hydrophobic	false
O2	NZ	LYS- 20	2.71	159.49	H-Bond (Protein Donor)	false
C8M	CB	PRO- 44	4.49	0	Hydrophobic	false
C7	CB	SER- 46	3.7	0	Hydrophobic	false
C4'	CB	ASN- 48	3.95	0	Hydrophobic	false
N3	OD1	ASN- 73	2.85	134.67	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 73	3.25	129.58	H-Bond (Protein Donor)	false
C7M	CE1	TYR- 141	4.24	0	Hydrophobic	false
C7M	CD1	ILE- 142	4.18	0	Hydrophobic	false
C8M	CD1	ILE- 142	3.51	0	Hydrophobic	false
C8M	CD1	ILE- 160	4.03	0	Hydrophobic	false
C7	CG2	ILE- 160	3.59	0	Hydrophobic	false
C9	CB	ILE- 160	3.79	0	Hydrophobic	false
O4	N	GLY- 162	3.36	134.26	H-Bond (Protein Donor)	false
N5	N	GLY- 162	2.78	152.03	H-Bond (Protein Donor)	false
O4	N	GLY- 163	2.93	149.89	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 198	3.55	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 198	2.93	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 198	2.93	131.25	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 200	3.23	138.47	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 200	3.19	146.37	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 200	3.1	151.37	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 200	3.59	0	Ionic (Protein Cationic)	false