scPDB - 2x86 entry

Protein Data Bank Entry:

PDB ID : 2x86

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-03-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-L-glycero-D-manno-heptose-6-epimerase
ID:	HLDD_ECO57
AC:	P67911
Organism:	Escherichia coli O157:H7
Reign:	Bacteria
TaxID:	83334
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.265
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.044	864.000

% Hydrophobic	% Polar
47.66	52.34
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	59.23 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
52.4335	-8.27252	103.839

Binding mode :

What is Poseview ?

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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
O1A	OG1	THR- 81	3.12	153.94	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 169	3.46	128.43	H-Bond (Protein Donor)	false
O3'	O	SER- 180	3.08	166.47	H-Bond (Ligand Donor)	false
C5'	CE	MET- 181	3.98	0	Hydrophobic	false
O2'	O	ALA- 182	2.91	178.78	H-Bond (Ligand Donor)	false
C2'	CG2	VAL- 184	3.88	0	Hydrophobic	false
C1'	CZ	PHE- 201	4.04	0	Hydrophobic	false
N1	N	PHE- 201	2.97	170.7	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 201	3.52	0	Aromatic Face/Face	false
N6	OG	SER- 204	2.89	155.71	H-Bond (Ligand Donor)	false
O1B	NH1	ARG- 209	2.66	150.27	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 209	2.75	173.01	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 209	3.76	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 209	3.59	0	Ionic (Protein Cationic)	false
N7	OH	TYR- 272	3.03	152.68	H-Bond (Protein Donor)	false