scPDB - 5f12 entry

Protein Data Bank Entry:

PDB ID : 5f12

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2015-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H dehydrogenase (quinone)
ID:	NQOR_ECOLI
AC:	P0A8G6
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
B	82 %

Ligand binding site composition:

B-Factor:	19.539
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.067	914.625

% Hydrophobic	% Polar
43.91	56.09
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	69.53 %
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
2.18965	-1.35197	18.7731

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	OG	SER- 9	2.7	154.53	H-Bond (Protein Donor)	false
O3P	N	MHO- 10	2.9	150.12	H-Bond (Protein Donor)	false
O1P	N	TYR- 11	3.16	124.69	H-Bond (Protein Donor)	false
O3P	N	TYR- 11	3.02	164.55	H-Bond (Protein Donor)	false
O1P	N	HIS- 13	2.85	164.34	H-Bond (Protein Donor)	false
O2P	N	ILE- 14	2.79	169.62	H-Bond (Protein Donor)	false
C5'	CB	PRO- 76	3.89	0	Hydrophobic	false
O2'	O	THR- 77	2.84	159.32	H-Bond (Ligand Donor)	false
C8	CD	ARG- 78	3.47	0	Hydrophobic	false
N5	N	PHE- 79	2.94	168.83	H-Bond (Protein Donor)	false
C7M	CE2	PHE- 79	4.18	0	Hydrophobic	false
C7M	CB	ASP- 91	4.16	0	Hydrophobic	false
C4'	CB	SER- 112	4.01	0	Hydrophobic	false
O4'	OG	SER- 112	2.75	156.6	H-Bond (Protein Donor)	false
N1	N	GLY- 114	3.03	153.55	H-Bond (Protein Donor)	false
O2	N	GLY- 116	2.99	142	H-Bond (Protein Donor)	false
N3	O	GLY- 117	2.76	154.29	H-Bond (Ligand Donor)	false
O3P	O	HOH- 326	2.7	161.85	H-Bond (Protein Donor)	false