scPDB - 1fdo entry

Protein Data Bank Entry:

PDB ID : 1fdo

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1997-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formate dehydrogenase H
ID:	FDHF_ECOLI
AC:	P07658
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.99.33

Chains:

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

Ligand binding site composition:

B-Factor:	23.106
Number of residues:	56
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.869	597.375

% Hydrophobic	% Polar
50.28	49.72
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	82.56 %
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
76.7197	41.2598	32.2087

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
O2A	N	ASN- 176	2.8	170.03	H-Bond (Protein Donor)	false
N19	O	ASP- 179	3.06	128.47	H-Bond (Ligand Donor)	false
O2A	OG	SER- 180	2.85	161.59	H-Bond (Protein Donor)	false
N22	O	SER- 180	2.82	158.41	H-Bond (Ligand Donor)	false
C23	CB	SER- 180	4.14	0	Hydrophobic	false
C11	CB	SER- 180	4.21	0	Hydrophobic	false
N2	O	CYS- 201	2.86	121.69	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 202	2.53	175.16	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 202	3.28	144.51	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 202	2.77	150.97	H-Bond (Ligand Donor)	false
O3'	NH1	ARG- 204	2.83	129.8	H-Bond (Protein Donor)	false
C2'	CD	ARG- 204	4.18	0	Hydrophobic	false
O6	N	GLY- 221	2.89	161.76	H-Bond (Protein Donor)	false
O6	ND2	ASN- 223	2.91	148.51	H-Bond (Protein Donor)	false
O1A	N	MET- 297	3.11	162.03	H-Bond (Protein Donor)	false
C10	CG	MET- 297	3.76	0	Hydrophobic	false
C3'	CG2	VAL- 580	4.33	0	Hydrophobic	false
O2B	NE	ARG- 581	2.98	157.14	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 581	3.2	140.54	H-Bond (Protein Donor)	false
O3B	NE	ARG- 581	3.44	120.64	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 581	3.53	0	Ionic (Protein Cationic)	false
C10	CD	ARG- 581	3.45	0	Hydrophobic	false
C23	CD	ARG- 581	3.93	0	Hydrophobic	false
N19	O	GLU- 582	2.56	133.14	H-Bond (Ligand Donor)	false
N18	O	HIS- 585	2.82	146.99	H-Bond (Ligand Donor)	false
C14	CE2	TYR- 586	3.4	0	Hydrophobic	false
O17	N	SER- 587	2.66	156.52	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 679	2.85	141.56	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 679	2.85	0	Ionic (Protein Cationic)	false
C2'	CD	LYS- 679	4.44	0	Hydrophobic	false