scPDB - 4qii entry

Protein Data Bank Entry:

PDB ID : 4qii

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2014-05-31

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_MYCTU
AC:	P9WNP5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	10 %
L	90 %

Ligand binding site composition:

B-Factor:	17.885
Number of residues:	51
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.411	934.875

% Hydrophobic	% Polar
57.40	42.60
According to VolSite

Ligand :

HET Code:	2NE
Formula:	C28H36N7O18P3S
Molecular weight:	883.608 g/mol
DrugBank ID:	-
Buried Surface Area:	58.06 %
Polar Surface area:	449.91 Å2

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

Mass center Coordinates

X	Y	Z
193.9	30.4501	258.514

Binding mode :

What is Poseview ?

2D View
3D View

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- 57	4.24	0	Hydrophobic	false
C03	CG	ARG- 58	4.49	0	Hydrophobic	false
C04	CD	ARG- 58	4.21	0	Hydrophobic	false
C14	CG	ARG- 58	3.86	0	Hydrophobic	false
O08	NE	ARG- 58	3.19	149.77	H-Bond (Protein Donor)	false
O08	NH2	ARG- 58	3.16	149.29	H-Bond (Protein Donor)	false
O08	CZ	ARG- 58	3.62	0	Ionic (Protein Cationic)	false
O23	NZ	LYS- 95	2.68	173.74	H-Bond (Protein Donor)	false
O23	NZ	LYS- 95	2.68	0	Ionic (Protein Cationic)	false
O25	NZ	LYS- 95	3.75	0	Ionic (Protein Cationic)	false
C03	CB	SER- 103	3.68	0	Hydrophobic	false
C42	CB	SER- 103	4.42	0	Hydrophobic	false
N31	O	SER- 103	3.27	152.11	H-Bond (Ligand Donor)	false
N45	O	SER- 103	2.7	160.28	H-Bond (Ligand Donor)	false
N31	O	GLY- 105	2.81	164.15	H-Bond (Ligand Donor)	false
O50	N	GLY- 105	2.88	157.91	H-Bond (Protein Donor)	false
N32	N	GLN- 107	2.99	162.31	H-Bond (Protein Donor)	false
C56	CE2	TYR- 115	2.59	0	Hydrophobic	false
C55	CD2	LEU- 134	3.87	0	Hydrophobic	false
C55	CG2	ILE- 136	4.3	0	Hydrophobic	false
C01	CE3	TRP- 157	3.67	0	Hydrophobic	false
C02	CD2	TRP- 157	4.29	0	Hydrophobic	false
C03	CB	TRP- 157	4.13	0	Hydrophobic	false
C04	CE2	TRP- 157	3.79	0	Hydrophobic	false
C03	CB	ALA- 159	3.95	0	Hydrophobic	false
C42	CB	ALA- 159	3.83	0	Hydrophobic	false
O50	N	GLY- 161	2.86	159.24	H-Bond (Protein Donor)	false
C01	CD	LYS- 182	4.38	0	Hydrophobic	false
C42	CB	THR- 184	4.08	0	Hydrophobic	false
O44	OG1	THR- 184	2.94	175.43	H-Bond (Protein Donor)	false
O53	OD1	ASP- 185	3.33	147.05	H-Bond (Ligand Donor)	false
C47	CG2	VAL- 188	3.72	0	Hydrophobic	false
S48	CB	SER- 190	3.51	0	Hydrophobic	false
O53	OG	SER- 190	2.87	149.98	H-Bond (Protein Donor)	false
C18	CZ	PHE- 299	4.19	0	Hydrophobic	false
C36	CE1	PHE- 299	4.33	0	Hydrophobic	false
O24	NZ	LYS- 302	2.83	161.7	H-Bond (Protein Donor)	false
O24	NZ	LYS- 302	2.83	0	Ionic (Protein Cationic)	false
O19	O	HOH- 683	2.85	146.11	H-Bond (Ligand Donor)	false