scPDB - 4koa entry

Protein Data Bank Entry:

PDB ID : 4koa

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2013-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1,5-anhydro-D-fructose reductase
ID:	AFR_RHIME
AC:	Q92KZ3
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	1.1.1.292

Chains:

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

Ligand binding site composition:

B-Factor:	32.222
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.795	722.250

% Hydrophobic	% Polar
35.51	64.49
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	47.08 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
19.3088	29.9616	-2.75971

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
O2X	N	ALA- 9	2.87	143.94	H-Bond (Protein Donor)	false
C5B	CB	SER- 10	4.33	0	Hydrophobic	false
C5D	CB	SER- 10	4.48	0	Hydrophobic	false
O2A	N	THR- 11	2.55	151.06	H-Bond (Protein Donor)	false
O1N	N	ILE- 12	2.62	152.1	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 12	3.75	0	Hydrophobic	false
O1X	OG	SER- 33	2.69	159.8	H-Bond (Protein Donor)	false
O3X	N	SER- 34	2.92	165.55	H-Bond (Protein Donor)	false
O3X	OG	SER- 34	2.96	168.26	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 38	3.43	137.6	H-Bond (Protein Donor)	false
O1X	NE	ARG- 38	3.04	161.01	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 38	3.34	140.79	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 38	3.4	154.58	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 38	3.64	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 38	3.82	161.64	Pi/Cation	false
C5D	CB	SER- 70	4.28	0	Hydrophobic	false
O3D	O	THR- 71	2.93	163.38	H-Bond (Ligand Donor)	false
C4B	CG2	THR- 72	4.32	0	Hydrophobic	false
O2D	OD1	ASN- 73	2.88	160.58	H-Bond (Ligand Donor)	false
C4D	CG	GLU- 93	4.14	0	Hydrophobic	false
O2D	NZ	LYS- 94	3.2	138.18	H-Bond (Protein Donor)	false