scPDB - 3koq entry

Protein Data Bank Entry:

PDB ID : 3koq

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2009-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative nitroreductase
ID:	Q180K0_PEPD6
AC:	Q180K0
Organism:	Peptoclostridium difficile
Reign:	Bacteria
TaxID:	272563
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	38 %
B	62 %

Ligand binding site composition:

B-Factor:	9.888
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.040	560.250

% Hydrophobic	% Polar
38.55	61.45
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	68.65 %
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
-4.18284	31.0842	12.308

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
O2P	NH1	ARG- 10	2.92	150.88	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 10	3.06	141.87	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 10	3.14	147.75	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 10	3.43	0	Ionic (Protein Cationic)	false
C1'	CB	SER- 12	4.15	0	Hydrophobic	false
C3'	CB	SER- 12	4.15	0	Hydrophobic	false
O1P	N	SER- 12	2.86	171.77	H-Bond (Protein Donor)	false
O2P	OG	SER- 12	2.7	158.24	H-Bond (Protein Donor)	false
N1	NH2	ARG- 14	3.06	162.2	H-Bond (Protein Donor)	false
O2	NE	ARG- 14	2.75	175.91	H-Bond (Protein Donor)	false
O2	NH2	ARG- 14	3.48	131.72	H-Bond (Protein Donor)	false
C8M	CB	PRO- 37	4.12	0	Hydrophobic	false
C4'	CB	ASN- 41	3.87	0	Hydrophobic	false
O2	OH	TYR- 66	2.6	140.42	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 91	3.96	0	Hydrophobic	false
C7M	CG2	ILE- 94	3.37	0	Hydrophobic	false
C7M	CD1	ILE- 98	4.17	0	Hydrophobic	false
C8M	CD1	ILE- 98	3.36	0	Hydrophobic	false
C1'	CG2	VAL- 115	3.94	0	Hydrophobic	false
C7M	CE2	TRP- 116	4.03	0	Hydrophobic	false
C8M	CD2	TRP- 116	4.36	0	Hydrophobic	false
C9	CB	TRP- 116	4.04	0	Hydrophobic	false
O4	N	CYS- 118	3.33	122.73	H-Bond (Protein Donor)	false
N5	N	CYS- 118	3.15	164.73	H-Bond (Protein Donor)	false
C7M	SG	CYS- 118	3.86	0	Hydrophobic	false
O4	N	TYR- 119	2.91	151.01	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 155	2.75	168.33	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 155	3.69	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 160	2.94	174.29	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 160	3.77	0	Ionic (Protein Cationic)	false