scPDB - 3rbv entry

Protein Data Bank Entry:

PDB ID : 3rbv

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sugar 3-ketoreductase
ID:	B3TMR8_9ACTN
AC:	B3TMR8
Organism:	Actinomadura kijaniata
Reign:	Bacteria
TaxID:	46161
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.313
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.256	540.000

% Hydrophobic	% Polar
40.63	59.38
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	57.77 %
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
9.28933	-28.8534	-27.8135

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
O2B	N	CYS- 17	3.28	136.05	H-Bond (Protein Donor)	false
O1X	N	CYS- 17	2.98	155.41	H-Bond (Protein Donor)	false
C5D	CB	ALA- 18	4.5	0	Hydrophobic	false
C5B	CB	ALA- 18	3.77	0	Hydrophobic	false
O1A	N	ASP- 19	2.87	165.11	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 19	2.79	170.56	H-Bond (Ligand Donor)	false
O1N	N	ILE- 20	2.86	178.81	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 20	4.02	0	Hydrophobic	false
C5D	CG2	ILE- 20	4.09	0	Hydrophobic	false
O2X	NE	ARG- 43	3.2	140.86	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 43	2.85	158.31	H-Bond (Protein Donor)	false
O3X	N	ARG- 43	3	168.48	H-Bond (Protein Donor)	false
O3X	NE	ARG- 43	3.28	153.07	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 43	3.47	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 43	3.76	22.25	Pi/Cation	false
O3X	OH	TYR- 63	2.55	140.18	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 79	3.7	0	Hydrophobic	false
C5B	CG	PRO- 80	4.19	0	Hydrophobic	false
C4D	CB	GLU- 101	3.88	0	Hydrophobic	false
O3D	O	LYS- 102	2.77	159.31	H-Bond (Ligand Donor)	false
O2D	O	LYS- 102	3.12	168.26	H-Bond (Ligand Donor)	false