scPDB - 3t88 entry

Protein Data Bank Entry:

PDB ID : 3t88

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1,4-dihydroxy-2-naphthoyl-CoA synthase
ID:	MENB_ECOLI
AC:	P0ABU0
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	16 %
D	84 %

Ligand binding site composition:

B-Factor:	19.257
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.388	604.125

% Hydrophobic	% Polar
60.89	39.11
According to VolSite

Ligand :

HET Code:	S0N
Formula:	C32H40N8O20P3
Molecular weight:	949.623 g/mol
DrugBank ID:	-
Buried Surface Area:	55.88 %
Polar Surface area:	473.61 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	6
Rings:	4
Aromatic rings:	3
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
-22.7852	70.8365	-21.7308

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
C17	CB	VAL- 44	4.18	0	Hydrophobic	false
C03	CG	ARG- 45	4.33	0	Hydrophobic	false
C04	CD	ARG- 45	4.1	0	Hydrophobic	false
C14	CG	ARG- 45	3.99	0	Hydrophobic	false
O07	NE	ARG- 45	3.04	158.96	H-Bond (Protein Donor)	false
O07	NH2	ARG- 45	3.27	142.49	H-Bond (Protein Donor)	false
O07	CZ	ARG- 45	3.6	0	Ionic (Protein Cationic)	false
C03	CB	SER- 84	3.74	0	Hydrophobic	false
C42	CB	SER- 84	4.4	0	Hydrophobic	false
N23	O	SER- 84	3	128.58	H-Bond (Ligand Donor)	false
N45	O	SER- 84	2.88	162.18	H-Bond (Ligand Donor)	false
N23	O	GLY- 86	2.96	154.25	H-Bond (Ligand Donor)	false
O50	N	GLY- 86	2.86	162.68	H-Bond (Protein Donor)	false
N24	N	GLN- 88	2.81	160.16	H-Bond (Protein Donor)	false
O35	NZ	LYS- 89	3.62	0	Ionic (Protein Cationic)	false
O62	OH	TYR- 97	2.73	147.63	H-Bond (Protein Donor)	false
C59	CD2	LEU- 106	3.76	0	Hydrophobic	false
C59	CG1	VAL- 108	3.76	0	Hydrophobic	false
C58	CD2	LEU- 109	3.31	0	Hydrophobic	false
C01	CD2	TYR- 129	3.8	0	Hydrophobic	false
C04	CE1	TYR- 129	3.64	0	Hydrophobic	false
C03	CG	TYR- 129	4.26	0	Hydrophobic	false
C01	CG1	ILE- 131	4.31	0	Hydrophobic	false
C03	CG1	ILE- 131	4.41	0	Hydrophobic	false
C42	CG2	ILE- 131	3.63	0	Hydrophobic	false
O50	N	GLY- 133	2.92	149.97	H-Bond (Protein Donor)	false
C42	CG2	THR- 155	4.49	0	Hydrophobic	false
O44	OG1	THR- 155	2.75	158.08	H-Bond (Protein Donor)	false
N48	OG	SER- 161	3.24	165.11	H-Bond (Ligand Donor)	false
C51	CB	SER- 161	4.24	0	Hydrophobic	false
C56	CB	ASP- 163	3.81	0	Hydrophobic	false
C57	CG2	THR- 254	3.91	0	Hydrophobic	false
O62	OH	TYR- 258	2.6	147.8	H-Bond (Protein Donor)	false
C28	CZ	PHE- 270	4.48	0	Hydrophobic	false