scPDB - 5eso entry

Protein Data Bank Entry:

PDB ID : 5eso

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2015-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
ID:	MEND_MYCTU
AC:	P9WK11
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	52 %
C	48 %

Ligand binding site composition:

B-Factor:	36.895
Number of residues:	27
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.953	1056.375

% Hydrophobic	% Polar
41.85	58.15
According to VolSite

Ligand :

HET Code:	ISC
Formula:	C10H8O6
Molecular weight:	224.167 g/mol
DrugBank ID:	DB02793
Buried Surface Area:	56.98 %
Polar Surface area:	109.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
67.2456	-13.356	23.6259

Binding mode :

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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
O1	N	SER- 29	3.04	162	H-Bond (Protein Donor)	false
C2	CB	SER- 29	3.99	0	Hydrophobic	false
O2	N	ARG- 30	2.95	136.94	H-Bond (Protein Donor)	false
O1	OG1	THR- 78	2.69	175.44	H-Bond (Protein Donor)	false
O2	OG1	THR- 78	3.42	124.91	H-Bond (Protein Donor)	false
O2	NH2	ARG- 107	3.12	140.08	H-Bond (Protein Donor)	false
O3	NH1	ARG- 107	2.99	160.34	H-Bond (Protein Donor)	false
O2	CZ	ARG- 107	3.79	0	Ionic (Protein Cationic)	false
O1	NE2	GLN- 118	3.14	158.96	H-Bond (Protein Donor)	false
O1'	CZ	ARG- 282	3.67	0	Ionic (Protein Cationic)	false
O2'	CZ	ARG- 282	3.85	0	Ionic (Protein Cationic)	false
O1'	NE	ARG- 282	2.92	163.46	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 282	3.08	163.5	H-Bond (Protein Donor)	false
O2	O	HOH- 786	2.78	179.96	H-Bond (Protein Donor)	false