scPDB - 4i42 entry

Protein Data Bank Entry:

PDB ID : 4i42

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2012-11-27

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
B	2 %
C	16 %
E	82 %

Ligand binding site composition:

B-Factor:	24.142
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)
1.342	1073.250

% Hydrophobic	% Polar
57.23	42.77
According to VolSite

Ligand :

HET Code:	1HA
Formula:	C32H38N7O18P3S
Molecular weight:	933.667 g/mol
DrugBank ID:	-
Buried Surface Area:	58.92 %
Polar Surface area:	449.91 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	5
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
1.77187	30.4078	-36.6758

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
CAA	CD1	ILE- 2	4.31	0	Hydrophobic	false
C1'	CB	VAL- 44	4.23	0	Hydrophobic	false
CBD	CG	ARG- 45	4.13	0	Hydrophobic	false
C5'	CG	ARG- 45	4.07	0	Hydrophobic	false
OAP	NH2	ARG- 45	3.22	139.68	H-Bond (Protein Donor)	false
OAP	NE	ARG- 45	2.93	160.05	H-Bond (Protein Donor)	false
OBN	NE	ARG- 45	3.45	121.79	H-Bond (Protein Donor)	false
OAP	CZ	ARG- 45	3.51	0	Ionic (Protein Cationic)	false
NBH	O	SER- 84	2.95	164.91	H-Bond (Ligand Donor)	false
N6	O	SER- 84	3.12	128.93	H-Bond (Ligand Donor)	false
CAB	CB	SER- 84	3.73	0	Hydrophobic	false
OAF	N	GLY- 86	2.91	168.43	H-Bond (Protein Donor)	false
N6	O	GLY- 86	3.02	161.33	H-Bond (Ligand Donor)	false
N1	N	GLN- 88	3.01	162.74	H-Bond (Protein Donor)	false
CAU	CD2	LEU- 106	3.72	0	Hydrophobic	false
CAW	CG1	VAL- 108	3.55	0	Hydrophobic	false
CAQ	CD2	LEU- 109	3.75	0	Hydrophobic	false
CCF	CD1	TYR- 129	4.47	0	Hydrophobic	false
CAA	CE1	TYR- 129	3.87	0	Hydrophobic	false
CAB	CG	TYR- 129	4.24	0	Hydrophobic	false
CBD	CE2	TYR- 129	3.84	0	Hydrophobic	false
CBB	CG2	ILE- 131	3.92	0	Hydrophobic	false
CAA	CG1	ILE- 131	4.37	0	Hydrophobic	false
CAB	CG1	ILE- 131	4.12	0	Hydrophobic	false
OAF	N	GLY- 133	2.76	135.42	H-Bond (Protein Donor)	false
OAD	OG1	THR- 155	2.62	146.05	H-Bond (Protein Donor)	false
CBB	CG2	THR- 155	4.32	0	Hydrophobic	false
CBA	CG2	VAL- 159	3.95	0	Hydrophobic	false
SBO	CB	SER- 161	3.86	0	Hydrophobic	false
CAV	CB	ASP- 163	4.13	0	Hydrophobic	false
CAR	CG2	THR- 254	3.5	0	Hydrophobic	false
CBZ	CE1	PHE- 270	4.46	0	Hydrophobic	false
OAN	NZ	LYS- 273	2.97	149.06	H-Bond (Protein Donor)	false
OAN	NZ	LYS- 273	2.97	0	Ionic (Protein Cationic)	false