scPDB - 3aw9 entry

Protein Data Bank Entry:

PDB ID : 3aw9

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent epimerase/dehydratase
ID:	A3MUJ4_PYRCJ
AC:	A3MUJ4
Organism:	Pyrobaculum calidifontis
Reign:	Archaea
TaxID:	410359
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.590
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.467	745.875

% Hydrophobic	% Polar
47.06	52.94
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	74.07 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-72.4762	19.8279	-26.9087

Binding mode :

What is Poseview ?

2D View
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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
C1'	CG1	VAL- 1071	3.84	0	Hydrophobic	false
C6'	CG1	VAL- 1071	4.05	0	Hydrophobic	false
O6'	N	VAL- 1071	3.27	147.36	H-Bond (Protein Donor)	false
O4'	OG	SER- 1109	2.77	147.28	H-Bond (Protein Donor)	false
O3'	OG	SER- 1110	2.78	136.68	H-Bond (Protein Donor)	false
C2'	CG2	THR- 1111	4.09	0	Hydrophobic	false
O4'	OH	TYR- 1133	3.29	148.4	H-Bond (Ligand Donor)	false
C6'	CE2	TYR- 1133	3.39	0	Hydrophobic	false
O1A	ND2	ASN- 1162	2.92	153.43	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 1162	3.21	120.95	H-Bond (Protein Donor)	false
C1D	CG2	VAL- 1172	4.49	0	Hydrophobic	false
C5D	CB	VAL- 1172	3.75	0	Hydrophobic	false
O2D	NE2	GLN- 1195	3.07	174.53	H-Bond (Protein Donor)	false
C4D	CG	GLN- 1195	4.13	0	Hydrophobic	false
O3D	NZ	LYS- 1197	3.17	138.35	H-Bond (Protein Donor)	false
O5D	NZ	LYS- 1197	3.19	139.06	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 1197	2.76	141.79	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 1197	2.76	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 1197	3.95	0	Ionic (Protein Cationic)	false
C1D	CG1	VAL- 1236	4.06	0	Hydrophobic	false
C4D	CG2	VAL- 1236	3.71	0	Hydrophobic	false
C2D	CH2	TRP- 1265	3.51	0	Hydrophobic	false
O2D	OD2	ASP- 1268	2.74	162.27	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 1268	2.88	147.05	H-Bond (Ligand Donor)	false
O3D	OD2	ASP- 1268	3.35	149.58	H-Bond (Ligand Donor)	false
C2'	CE	MET- 1272	4.38	0	Hydrophobic	false
C4'	C4N	NAD- 1901	3.74	0	Hydrophobic	false