scPDB - 2fr1 entry

Protein Data Bank Entry:

PDB ID : 2fr1

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2006-01-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-deoxyerythronolide-B synthase EryA1, modules 1 and 2
ID:	ERYA1_SACER
AC:	Q03131
Organism:	Saccharopolyspora erythraea
Reign:	Bacteria
TaxID:	1836
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.173
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.779	388.125

% Hydrophobic	% Polar
43.48	56.52
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	52.16 %
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
-1.4616	17.6407	29.2474

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
O3	O	HOH- 207	3.26	138.22	H-Bond (Protein Donor)	false
O2A	N	GLY- 1676	3.48	147.55	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 1677	3.42	0	Hydrophobic	false
C2B	CB	SER- 1697	3.67	0	Hydrophobic	false
O2X	OG	SER- 1699	2.69	160.48	H-Bond (Protein Donor)	false
O3X	N	SER- 1699	2.72	125.82	H-Bond (Protein Donor)	false
O3X	N	GLY- 1700	3.24	127.38	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 1726	2.83	153.18	H-Bond (Ligand Donor)	false
N1A	N	VAL- 1727	2.91	159.54	H-Bond (Protein Donor)	false
C5D	CB	ALA- 1752	4.5	0	Hydrophobic	false
C3D	CB	ALA- 1754	4.42	0	Hydrophobic	false
O3D	NZ	LYS- 1776	3.46	153.49	H-Bond (Protein Donor)	false
O2D	O	SER- 1799	3.26	139.59	H-Bond (Ligand Donor)	false
O3D	OH	TYR- 1813	3.04	143.46	H-Bond (Protein Donor)	false
C2D	CZ	TYR- 1813	3.92	0	Hydrophobic	false