scPDB - 3hdy entry

Protein Data Bank Entry:

PDB ID : 3hdy

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-05-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	Q9RYF1_DEIRA
AC:	Q9RYF1
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.215
Number of residues:	59
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.846	1238.625

% Hydrophobic	% Polar
45.23	54.77
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	71.86 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
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
-2.58179	-58.4727	-80.4976

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- 40	3.14	152.65	H-Bond (Protein Donor)	false
N3A	N	ARG- 60	3.21	154.43	H-Bond (Protein Donor)	false
O1A	N	ASN- 67	3.19	174.92	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 67	3.42	143.89	H-Bond (Protein Donor)	false
C2'	CB	ASN- 67	4.49	0	Hydrophobic	false
O2'	NE2	HIS- 85	3.03	152.7	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 85	4	0	Aromatic Face/Face	false
N3	O	ILE- 86	3.01	160.47	H-Bond (Ligand Donor)	false
O4	N	ILE- 86	3.1	172.53	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 242	3.2	161.02	H-Bond (Ligand Donor)	false
N1A	N	TYR- 243	3.38	156.36	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 277	3.59	0	Hydrophobic	false
C7M	CZ	PHE- 279	4.03	0	Hydrophobic	false
C8M	CB	TYR- 334	3.71	0	Hydrophobic	false
C3'	CD	ARG- 364	4.38	0	Hydrophobic	false
C5'	CB	ARG- 364	4.27	0	Hydrophobic	false
O1P	N	ARG- 364	3.06	159.45	H-Bond (Protein Donor)	false
C5B	CD1	LEU- 365	4.29	0	Hydrophobic	false
O3'	O	TYR- 371	2.94	151.86	H-Bond (Ligand Donor)	false
O2	N	MET- 373	2.85	163.55	H-Bond (Protein Donor)	false
C2'	CG	MET- 373	4.12	0	Hydrophobic	false
C5'	CG2	VAL- 376	3.7	0	Hydrophobic	false
O1P	O	HOH- 398	2.93	179.95	H-Bond (Protein Donor)	false