scPDB - 4jd3 entry

Protein Data Bank Entry:

PDB ID : 4jd3

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2013-02-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-pyrone synthesis polyketide synthase-like Pks11
ID:	PKS11_MYCTU
AC:	P9WPF3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	35.952
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.569	756.000

% Hydrophobic	% Polar
63.84	36.16
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	48.81 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
38.6096	-22.7156	90.1118

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
C5B	CD1	LEU- 41	4.28	0	Hydrophobic	false
CDP	CG	LEU- 41	4.13	0	Hydrophobic	false
CCP	CB	ALA- 44	3.92	0	Hydrophobic	false
CEP	CB	ALA- 44	4.01	0	Hydrophobic	false
CEP	CB	ALA- 45	3.95	0	Hydrophobic	false
S1P	CB	SER- 138	4.15	0	Hydrophobic	false
C1B	CG1	VAL- 179	4.03	0	Hydrophobic	false
N1A	OG	SER- 180	3.32	163.98	H-Bond (Protein Donor)	false
CDP	CG2	VAL- 183	3.68	0	Hydrophobic	false
CAP	CD1	LEU- 187	4.06	0	Hydrophobic	false
C2P	CZ	PHE- 188	3.81	0	Hydrophobic	false
S1P	CE1	PHE- 188	3.81	0	Hydrophobic	false
C2P	SD	MET- 228	4.08	0	Hydrophobic	false
N6A	O	LEU- 241	3.11	139.61	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 282	3.9	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 282	2.79	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 282	2.79	151.27	H-Bond (Protein Donor)	false
C6P	CG2	VAL- 283	3.25	0	Hydrophobic	false