scPDB - 1r6w entry

Protein Data Bank Entry:

PDB ID : 1r6w

Resolution :1.620 Å

Experimental Method : X-ray

Deposition Date : 2003-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	o-succinylbenzoate synthase
ID:	MENC_ECOLI
AC:	P29208
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.116
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.583	651.375

% Hydrophobic	% Polar
48.19	51.81
According to VolSite

Ligand :

HET Code:	164
Formula:	C11H10O6
Molecular weight:	238.194 g/mol
DrugBank ID:	DB06864
Buried Surface Area:	60.64 %
Polar Surface area:	117.56 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:	5

Mass center Coordinates

X	Y	Z
27.9018	20.5851	13.1307

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
C3	CZ	PHE- 51	4.21	0	Hydrophobic	false
C10	CD2	LEU- 109	4.43	0	Hydrophobic	false
O1	NZ	LYS- 131	2.96	138.38	H-Bond (Protein Donor)	false
O5	NZ	LYS- 131	2.98	155.76	H-Bond (Protein Donor)	false
O1	NZ	LYS- 131	2.96	0	Ionic (Protein Cationic)	false
O5	NZ	LYS- 131	2.98	0	Ionic (Protein Cationic)	false
O4	NZ	LYS- 131	3.74	0	Ionic (Protein Cationic)	false
O2	ND2	ASN- 163	2.79	141.55	H-Bond (Protein Donor)	false
O1	NZ	LYS- 235	2.99	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 235	3.28	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 235	3.28	124.14	H-Bond (Protein Donor)	false
O5	OG	SER- 262	2.69	157.76	H-Bond (Protein Donor)	false
C9	CB	SER- 263	4.25	0	Hydrophobic	false
C9	CG2	THR- 291	4.22	0	Hydrophobic	false
O1	MG	MG- 736	2.15	0	Metal Acceptor	false
O2	MG	MG- 736	2.08	0	Metal Acceptor	false
O4	O	HOH- 773	2.75	135.08	H-Bond (Protein Donor)	false