scPDB - 3rno entry

Protein Data Bank Entry:

PDB ID : 3rno

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-04-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H-hydrate epimerase
ID:	NNRE_MOUSE
AC:	Q8K4Z3
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	5.1.99.6

Chains:

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

Ligand binding site composition:

B-Factor:	60.536
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.237	459.000

% Hydrophobic	% Polar
45.59	54.41
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	55.03 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.8991	17.4616	31.0374

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
C1B	CG	PRO- 87	3.78	0	Hydrophobic	false
O1N	N	ASN- 89	2.6	167.51	H-Bond (Protein Donor)	false
C4D	CB	ASN- 89	3.93	0	Hydrophobic	false
O2A	N	ASN- 90	3.18	164.42	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 90	3.29	136.36	H-Bond (Protein Donor)	false
C4D	CB	ASN- 90	4.44	0	Hydrophobic	false
N1N	OD1	ASP- 93	3.84	0	Ionic (Ligand Cationic)	false
N1N	OD2	ASP- 93	3.09	0	Ionic (Ligand Cationic)	false
N1N	OD2	ASP- 93	3.09	132.93	H-Bond (Ligand Donor)	false
O1X	NZ	LYS- 114	3.23	145	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 114	3.23	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 114	3.12	0	Ionic (Protein Cationic)	false
C1B	CE1	PHE- 158	4.44	0	Hydrophobic	false
C3D	CD1	PHE- 160	3.46	0	Hydrophobic	false
C2D	CE1	PHE- 160	3.83	0	Hydrophobic	false
C5D	CE1	PHE- 160	4.19	0	Hydrophobic	false
O3D	N	PHE- 160	3.41	149.55	H-Bond (Protein Donor)	false
O3	OG	SER- 161	2.83	151.13	H-Bond (Protein Donor)	false
N6A	O	LYS- 163	3.03	148.93	H-Bond (Ligand Donor)	false
N1A	N	ARG- 167	3.19	147.9	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 167	3.81	156.41	Pi/Cation	false
O3D	OD2	ASP- 188	2.93	162.43	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 188	2.77	148.46	H-Bond (Ligand Donor)	false
C2D	CD1	LEU- 211	4.48	0	Hydrophobic	false
O2A	O	HOH- 270	2.6	179.95	H-Bond (Protein Donor)	false