scPDB - 1vdc entry

Protein Data Bank Entry:

PDB ID : 1vdc

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1996-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thioredoxin reductase 1, mitochondrial
ID:	TRXB1_ARATH
AC:	Q39243
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	1.8.1.9

Chains:

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

Ligand binding site composition:

B-Factor:	26.265
Number of residues:	73
Including
Standard Amino Acids:	67
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.042	567.000

% Hydrophobic	% Polar
48.81	51.19
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.63 %
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
23.0566	69.8975	57.5516

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
O4B	N	SER- 13	3.11	138.32	H-Bond (Protein Donor)	false
O2P	N	ALA- 16	2.99	156.03	H-Bond (Protein Donor)	false
C2B	CB	ALA- 36	4.02	0	Hydrophobic	false
C3B	CG2	ILE- 37	4.23	0	Hydrophobic	false
C2B	CB	ILE- 37	4.46	0	Hydrophobic	false
O2A	N	GLN- 42	3.21	134.88	H-Bond (Protein Donor)	false
C6	CB	THR- 46	3.78	0	Hydrophobic	false
N3	OD1	ASN- 51	2.81	155.84	H-Bond (Ligand Donor)	false
N6A	O	VAL- 84	3.04	157.94	H-Bond (Ligand Donor)	false
N1A	N	VAL- 84	3.13	158.74	H-Bond (Protein Donor)	false
C8M	CB	ALA- 116	3.81	0	Hydrophobic	false
C7M	CZ2	TRP- 129	3.73	0	Hydrophobic	false
C7M	CB	ALA- 134	4.32	0	Hydrophobic	false
C8M	CB	ALA- 134	4.1	0	Hydrophobic	false
C8	CB	CYS- 135	4	0	Hydrophobic	false
C6	SG	CYS- 138	4.21	0	Hydrophobic	false
C1'	SG	CYS- 138	4.11	0	Hydrophobic	false
C9A	SG	CYS- 138	3.47	0	Hydrophobic	false
C5'	CB	ASP- 286	4.14	0	Hydrophobic	false
O1P	N	ASP- 286	2.76	161.07	H-Bond (Protein Donor)	false
N1	N	ALA- 295	3.49	145.03	H-Bond (Protein Donor)	false
O2	N	ALA- 295	2.72	159.45	H-Bond (Protein Donor)	false
C5'	CB	ALA- 298	3.69	0	Hydrophobic	false
O2A	O	HOH- 507	2.93	179.98	H-Bond (Protein Donor)	false
O2B	O	HOH- 516	3.09	155.76	H-Bond (Ligand Donor)	false
O1A	O	HOH- 519	2.58	179.96	H-Bond (Protein Donor)	false
O4	O	HOH- 524	2.64	179.96	H-Bond (Protein Donor)	false
O1P	O	HOH- 630	2.57	163.47	H-Bond (Protein Donor)	false