scPDB - 3he3 entry

Protein Data Bank Entry:

PDB ID : 3he3

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
E	100 %

Ligand binding site composition:

B-Factor:	47.972
Number of residues:	63
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.877	1292.625

% Hydrophobic	% Polar
38.38	61.62
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.18 %
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
-23.1654	-117.009	94.1166

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
O1P	N	ALA- 40	3.01	147.91	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 59	2.8	167.1	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 59	2.74	162.01	H-Bond (Ligand Donor)	false
N3A	N	ARG- 60	3.18	151.86	H-Bond (Protein Donor)	false
C2B	CG	ARG- 60	4.41	0	Hydrophobic	false
O3B	NH1	ARG- 61	2.85	148.46	H-Bond (Protein Donor)	false
C2B	CD	ARG- 61	4.31	0	Hydrophobic	false
O2A	N	ASN- 67	3.18	163.55	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 85	3.03	127.92	H-Bond (Protein Donor)	false
N3	O	ILE- 86	2.82	137.22	H-Bond (Ligand Donor)	false
O4	N	ILE- 86	3.02	165.42	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 242	3.14	147.19	H-Bond (Ligand Donor)	false
N1A	N	TYR- 243	3.2	164.71	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 277	3.68	0	Hydrophobic	false
C7M	CE2	PHE- 279	4.27	0	Hydrophobic	false
C8M	CB	TYR- 334	3.73	0	Hydrophobic	false
C3'	CD	ARG- 364	4.41	0	Hydrophobic	false
C5'	CB	ARG- 364	4.23	0	Hydrophobic	false
O2P	N	ARG- 364	2.95	166.63	H-Bond (Protein Donor)	false
O3'	O	TYR- 371	2.93	174.56	H-Bond (Ligand Donor)	false
N1	N	MET- 373	3.43	141.25	H-Bond (Protein Donor)	false
O2	N	MET- 373	2.86	160.59	H-Bond (Protein Donor)	false
C2'	CG	MET- 373	3.8	0	Hydrophobic	false
C5'	CG2	VAL- 376	3.55	0	Hydrophobic	false
O2	O	HOH- 404	2.63	179.96	H-Bond (Protein Donor)	false
O3P	O	HOH- 405	3.33	164.14	H-Bond (Protein Donor)	false
O1P	O	HOH- 413	2.79	160.99	H-Bond (Protein Donor)	false
O2A	O	HOH- 421	2.75	158.87	H-Bond (Protein Donor)	false
N5	O	HOH- 593	3.07	179.97	H-Bond (Protein Donor)	false