scPDB - 5ej8 entry

Protein Data Bank Entry:

PDB ID : 5ej8

Resolution :1.340 Å

Experimental Method : X-ray

Deposition Date : 2015-11-01

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_ECOLI
AC:	P17109
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	29 %
F	71 %

Ligand binding site composition:

B-Factor:	10.873
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.801	1728.000

% Hydrophobic	% Polar
45.31	54.69
According to VolSite

Ligand :

HET Code:	TD6
Formula:	C16H21N4O10P2S
Molecular weight:	523.371 g/mol
DrugBank ID:	-
Buried Surface Area:	80.72 %
Polar Surface area:	285.67 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-16.449	59.9706	62.7866

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
CM4	CG	PRO- 30	3.61	0	Hydrophobic	false
N1'	OE1	GLU- 55	3.09	135.49	H-Bond (Ligand Donor)	false
N1'	OE2	GLU- 55	2.93	162.97	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 78	4.01	0	Hydrophobic	false
CM2	CB	ALA- 82	4.4	0	Hydrophobic	false
OL2	ND2	ASN- 117	2.97	153.42	H-Bond (Protein Donor)	false
S1	CB	SER- 391	3.51	0	Hydrophobic	false
C7	CB	SER- 391	3.85	0	Hydrophobic	false
O3B	OG	SER- 391	2.55	163.52	H-Bond (Protein Donor)	false
OL3	N	SER- 391	2.77	159.39	H-Bond (Protein Donor)	false
O2B	N	LEU- 392	2.99	152.82	H-Bond (Protein Donor)	false
OL2	CZ	ARG- 395	3.57	0	Ionic (Protein Cationic)	false
OL3	CZ	ARG- 395	3.73	0	Ionic (Protein Cationic)	false
OL2	NH2	ARG- 395	2.83	169.65	H-Bond (Protein Donor)	false
OL2	NH1	ARG- 395	3.42	133.33	H-Bond (Protein Donor)	false
OL3	NH1	ARG- 395	2.84	163.49	H-Bond (Protein Donor)	false
OL2	NH1	ARG- 413	3.34	141.02	H-Bond (Protein Donor)	false
OL2	NH2	ARG- 413	3.41	138.33	H-Bond (Protein Donor)	false
OL3	NH2	ARG- 413	2.83	162.9	H-Bond (Protein Donor)	false
OL2	CZ	ARG- 413	3.8	0	Ionic (Protein Cationic)	false
OL3	CZ	ARG- 413	3.83	0	Ionic (Protein Cationic)	false
C13	CB	SER- 416	3.88	0	Hydrophobic	false
N4'	O	SER- 416	3.07	158.34	H-Bond (Ligand Donor)	false
S1	CG2	ILE- 418	4.32	0	Hydrophobic	false
C5'	CG1	ILE- 418	4.29	0	Hydrophobic	false
CM2	CG1	ILE- 418	4.12	0	Hydrophobic	false
CM4	CD1	ILE- 418	3.81	0	Hydrophobic	false
C7	CD1	ILE- 418	4.01	0	Hydrophobic	false
N3'	N	ILE- 418	3.05	164.56	H-Bond (Protein Donor)	false
CM2	CB	ASP- 419	3.69	0	Hydrophobic	false
C6	CD1	LEU- 443	4.28	0	Hydrophobic	false
C7	CB	LEU- 443	4.2	0	Hydrophobic	false
O1A	N	LEU- 443	3.02	167.58	H-Bond (Protein Donor)	false
O2A	OG	SER- 444	2.78	158.98	H-Bond (Protein Donor)	false
O2A	N	SER- 444	2.98	148.25	H-Bond (Protein Donor)	false
CM2	CE2	TYR- 447	3.74	0	Hydrophobic	false
O1B	ND2	ASN- 469	3.02	145.43	H-Bond (Protein Donor)	false
O1B	N	GLN- 473	2.95	156.84	H-Bond (Protein Donor)	false
S1	CG2	ILE- 474	3.72	0	Hydrophobic	false
C6	CG2	ILE- 474	4.45	0	Hydrophobic	false
CLB	CD1	ILE- 474	4.32	0	Hydrophobic	false
O3B	N	ILE- 474	3.03	169.32	H-Bond (Protein Donor)	false
C6	CE2	PHE- 475	4.1	0	Hydrophobic	false
CM4	CE2	PHE- 475	4.18	0	Hydrophobic	false
O1A	MN	MN- 603	2.08	0	Metal Acceptor	false
O1B	MN	MN- 603	2.16	0	Metal Acceptor	false
O2B	O	HOH- 921	2.77	161.37	H-Bond (Protein Donor)	false