scPDB - 1d4c entry

Protein Data Bank Entry:

PDB ID : 1d4c

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 1999-10-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Fumarate reductase flavoprotein subunit
ID:	FRDA_SHEON
AC:	P83223
Organism:	Shewanella oneidensis
Reign:	Bacteria
TaxID:	211586
EC Number:	1.3.5.4

Chains:

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

Ligand binding site composition:

B-Factor:	20.701
Number of residues:	70
Including
Standard Amino Acids:	65
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.131	725.625

% Hydrophobic	% Polar
49.30	50.70
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.61 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.2906	71.8413	3.18841

Binding mode :

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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	N	ALA- 136	3.11	141.2	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 155	2.97	145.59	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 155	3.03	140.83	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 155	2.95	161.75	H-Bond (Ligand Donor)	false
C1B	CB	LYS- 156	4.46	0	Hydrophobic	false
O1A	N	ASN- 163	3.5	161.02	H-Bond (Protein Donor)	false
O2A	N	ASN- 163	2.73	128.57	H-Bond (Protein Donor)	false
C8M	CB	ASN- 163	4.16	0	Hydrophobic	false
C4'	CB	ASN- 163	4.15	0	Hydrophobic	false
O2A	N	THR- 164	2.72	151.35	H-Bond (Protein Donor)	false
O2A	OG1	THR- 164	2.99	150.05	H-Bond (Protein Donor)	false
O4'	OG1	THR- 164	3.11	149.99	H-Bond (Ligand Donor)	false
C7M	CB	LEU- 166	3.76	0	Hydrophobic	false
C6	CB	ALA- 167	4.02	0	Hydrophobic	false
C9A	CB	ALA- 167	4.07	0	Hydrophobic	false
O4	N	GLY- 169	2.66	133.77	H-Bond (Protein Donor)	false
N3	O	GLY- 170	3.11	150.95	H-Bond (Ligand Donor)	false
N6A	O	VAL- 277	3.18	168.65	H-Bond (Ligand Donor)	false
N1A	N	VAL- 277	3.04	128.5	H-Bond (Protein Donor)	false
C7M	CB	THR- 335	4.45	0	Hydrophobic	false
C8M	CB	THR- 335	4.42	0	Hydrophobic	false
C7M	CE	MET- 374	3.56	0	Hydrophobic	false
C6	CE	MET- 374	3.74	0	Hydrophobic	false
C5'	CB	GLU- 534	4.28	0	Hydrophobic	false
O1P	N	GLU- 534	2.95	159.07	H-Bond (Protein Donor)	false
C3'	CB	ALA- 549	3.46	0	Hydrophobic	false
C1'	CB	ALA- 549	3.21	0	Hydrophobic	false
O2	N	ILE- 550	2.8	162.94	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 550	4.13	0	Hydrophobic	false
C5'	CG2	ILE- 553	3.68	0	Hydrophobic	false
O2P	O	HOH- 822	2.71	179.98	H-Bond (Protein Donor)	false
O1P	O	HOH- 844	2.95	165.86	H-Bond (Protein Donor)	false