scPDB - 1h5n entry

Protein Data Bank Entry:

PDB ID : 1h5n

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-05-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dimethyl sulfoxide/trimethylamine N-oxide reductase
ID:	DSTOR_RHOCA
AC:	Q52675
Organism:	Rhodobacter capsulatus
Reign:	Bacteria
TaxID:	1061
EC Number:	1.7.2.3

Chains:

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

Ligand binding site composition:

B-Factor:	12.943
Number of residues:	64
Including
Standard Amino Acids:	58
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.805	526.500

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	PGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	82.43 %
Polar Surface area:	444.81 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	10
Rings:	6
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
8.67223	64.565	-23.835

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
S12	CE2	TYR- 114	3.84	0	Hydrophobic	false
C11	CE2	TYR- 114	4.03	0	Hydrophobic	false
O2A	N	TRP- 116	2.64	138.91	H-Bond (Protein Donor)	false
C11	CB	TYR- 146	4.02	0	Hydrophobic	false
S12	CB	TYR- 146	4.32	0	Hydrophobic	false
S13	CB	TYR- 146	4.01	0	Hydrophobic	false
C14	CB	TYR- 146	3.61	0	Hydrophobic	false
C23	CD2	TYR- 146	3.73	0	Hydrophobic	false
S13	CB	SER- 147	3.83	0	Hydrophobic	false
S13	CD	ARG- 326	4.39	0	Hydrophobic	false
C14	CD	ARG- 326	4.27	0	Hydrophobic	false
O17	NH1	ARG- 326	3.36	130.36	H-Bond (Protein Donor)	false
N3	N	GLY- 432	3.47	124.47	H-Bond (Protein Donor)	false
O1A	N	ASN- 434	2.58	157.12	H-Bond (Protein Donor)	false
N22	O	HIS- 438	2.96	151.74	H-Bond (Ligand Donor)	false
C23	CB	HIS- 438	3.85	0	Hydrophobic	false
C11	CB	HIS- 438	3.86	0	Hydrophobic	false
N20	NE2	GLN- 440	3.35	121.49	H-Bond (Protein Donor)	false
N2	O	HIS- 458	3.07	178.93	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 459	2.69	162.73	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 459	2.74	169.33	H-Bond (Ligand Donor)	false
O6	NH1	ARG- 481	2.91	166	H-Bond (Protein Donor)	false
N1	OD2	ASP- 511	2.73	172.97	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 511	3.5	127.92	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 511	2.77	162.46	H-Bond (Ligand Donor)	false
N18	O	ALA- 641	2.98	134.94	H-Bond (Ligand Donor)	false
N15	NE2	HIS- 643	3.03	156.11	H-Bond (Ligand Donor)	false
C10	CB	HIS- 649	4.21	0	Hydrophobic	false
O1B	N	SER- 650	2.71	139.44	H-Bond (Protein Donor)	false
O2B	NE2	GLN- 651	2.75	164.38	H-Bond (Protein Donor)	false
C5'	CG	GLN- 651	4.11	0	Hydrophobic	false
C3'	CG	GLN- 651	3.81	0	Hydrophobic	false
N19	OD1	ASN- 737	2.92	165.41	H-Bond (Ligand Donor)	false
N20	ND2	ASN- 737	3.11	160.3	H-Bond (Protein Donor)	false
O17	NE2	GLN- 755	3.19	155.96	H-Bond (Protein Donor)	false
O6	O	HOH- 2577	2.79	179.99	H-Bond (Protein Donor)	false