scPDB - 1d4d entry

Protein Data Bank Entry:

PDB ID : 1d4d

Resolution :2.500 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
A	100 %

Ligand binding site composition:

B-Factor:	30.377
Number of residues:	78
Including
Standard Amino Acids:	69
Non Standard Amino Acids:	1
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.129	583.875

% Hydrophobic	% Polar
48.55	51.45
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.5 %
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
2.59016	42.1708	15.6653

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	N	ALA- 136	2.95	164.2	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 155	2.94	167.73	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 155	3.49	136.11	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 155	2.84	158.9	H-Bond (Ligand Donor)	false
N3A	N	LYS- 156	3.25	131.32	H-Bond (Protein Donor)	false
O1A	N	ASN- 163	3.11	170.82	H-Bond (Protein Donor)	false
C4'	CB	ASN- 163	4.17	0	Hydrophobic	false
C8M	CB	ASN- 163	3.81	0	Hydrophobic	false
O2A	N	THR- 164	2.69	168.16	H-Bond (Protein Donor)	false
O2A	OG1	THR- 164	2.55	173.55	H-Bond (Protein Donor)	false
O4'	OG1	THR- 164	3.27	172.28	H-Bond (Ligand Donor)	false
C7M	CB	LEU- 166	3.96	0	Hydrophobic	false
N3	O	GLY- 170	2.7	169.89	H-Bond (Ligand Donor)	false
O4	N	GLY- 170	3.2	121.54	H-Bond (Protein Donor)	false
N6A	O	VAL- 277	3.08	174.64	H-Bond (Ligand Donor)	false
N1A	N	VAL- 277	2.89	162.15	H-Bond (Protein Donor)	false
C7M	CB	THR- 335	4.21	0	Hydrophobic	false
C8M	CB	THR- 335	4.45	0	Hydrophobic	false
C6	CE	MET- 374	3.57	0	Hydrophobic	false
C7M	SD	MET- 374	3.72	0	Hydrophobic	false
O3'	ND1	HIS- 504	3.05	122.01	H-Bond (Protein Donor)	false
C5'	CB	GLU- 534	4.01	0	Hydrophobic	false
O1P	N	GLU- 534	2.86	161.51	H-Bond (Protein Donor)	false
O2	N	ILE- 550	2.88	174.24	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 550	3.98	0	Hydrophobic	false
C4'	CD1	ILE- 553	4.46	0	Hydrophobic	false
C5'	CG2	ILE- 553	4.23	0	Hydrophobic	false
O1A	O	HOH- 702	3.03	161.46	H-Bond (Protein Donor)	false
N7A	O	HOH- 704	2.81	177.77	H-Bond (Protein Donor)	false
O2P	O	HOH- 705	2.6	179.95	H-Bond (Protein Donor)	false
O3B	O	HOH- 706	3.16	126.46	H-Bond (Protein Donor)	false
O1P	O	HOH- 726	2.81	179.96	H-Bond (Protein Donor)	false