scPDB - 1kqf entry

Protein Data Bank Entry:

PDB ID : 1kqf

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2002-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formate dehydrogenase, nitrate-inducible, major subunit
ID:	FDNG_ECOLI
AC:	P24183
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.5.6

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	14.430
Number of residues:	65
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.778	492.750

% Hydrophobic	% Polar
52.05	47.95
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	76.51 %
Polar Surface area:	440.93 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	10
Rings:	6
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-1.6353	51.0753	116.767

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
O1A	NE2	GLN- 192	2.82	158.88	H-Bond (Protein Donor)	false
S12	CB	GLN- 192	3.74	0	Hydrophobic	false
C10	CG	GLN- 192	4.23	0	Hydrophobic	false
C11	CG2	VAL- 195	4.24	0	Hydrophobic	false
C23	CG2	VAL- 195	3.91	0	Hydrophobic	false
S13	SG	CYS- 196	3.32	0	Hydrophobic	false
S13	CD1	LEU- 410	3.53	0	Hydrophobic	false
O1A	NE2	HIS- 448	2.87	153.24	H-Bond (Protein Donor)	false
O2A	N	ASN- 558	2.76	162.87	H-Bond (Protein Donor)	false
O2A	OG	SER- 562	2.98	163.05	H-Bond (Protein Donor)	false
N22	O	SER- 562	2.82	169.79	H-Bond (Ligand Donor)	false
C23	CB	SER- 562	3.91	0	Hydrophobic	false
C11	CB	SER- 562	3.71	0	Hydrophobic	false
N2	O	ILE- 582	3.18	153.38	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 583	2.67	159.16	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 583	3.09	135.54	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 583	2.87	174.07	H-Bond (Ligand Donor)	false
C1'	CG	PRO- 584	4.29	0	Hydrophobic	false
N1	OD2	ASP- 649	2.71	169.87	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 649	2.81	175.94	H-Bond (Ligand Donor)	false
N18	OG1	THR- 894	2.95	136.8	H-Bond (Ligand Donor)	false
N19	OG1	THR- 894	3.08	127.01	H-Bond (Ligand Donor)	false
O17	NH1	ARG- 896	2.9	156.97	H-Bond (Protein Donor)	false
O2B	ND1	HIS- 902	2.63	164.2	H-Bond (Protein Donor)	false
C3'	CE3	TRP- 904	4.2	0	Hydrophobic	false
C2'	CD2	TRP- 904	3.81	0	Hydrophobic	false
N19	OD1	ASN- 989	2.86	154.66	H-Bond (Ligand Donor)	false
N20	ND2	ASN- 989	3.22	146.84	H-Bond (Protein Donor)	false
C14	CE2	TYR- 1005	4.19	0	Hydrophobic	false
O4'	O	HOH- 1029	2.88	179.95	H-Bond (Protein Donor)	false
N7	O	HOH- 1032	2.7	155.91	H-Bond (Protein Donor)	false
O1B	O	HOH- 1145	2.71	149.21	H-Bond (Protein Donor)	false