scPDB - 4qvh entry

Protein Data Bank Entry:

PDB ID : 4qvh

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2014-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphopantetheinyl transferase PptT (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl-carrier protein]pantetheinephosphotransferase)
ID:	O33336_MYCTU
AC:	O33336
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.475
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.057	631.125

% Hydrophobic	% Polar
36.36	63.64
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	70.54 %
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
89.2491	45.115	170.084

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
O7A	NH1	ARG- 419	3.02	158.3	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 419	3.35	125.6	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 419	2.87	138.9	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 419	3.8	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 419	3.49	0	Ionic (Protein Cationic)	false
O7A	CZ	ARG- 427	3.98	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 427	3.55	0	Ionic (Protein Cationic)	false
O7A	NH1	ARG- 427	3.05	166.53	H-Bond (Protein Donor)	false
O8A	NH1	ARG- 427	3.46	129.45	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 427	2.76	166.27	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 446	3.59	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 446	2.71	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 446	2.71	170.04	H-Bond (Protein Donor)	false
N6A	O	LYS- 449	3.08	148.86	H-Bond (Ligand Donor)	false
O2A	OG1	THR- 463	2.56	171.02	H-Bond (Protein Donor)	false
O7A	NE2	HIS- 464	2.71	176.89	H-Bond (Protein Donor)	false
O1A	N	HIS- 464	2.96	158.35	H-Bond (Protein Donor)	false
O4A	OD2	ASP- 485	2.58	163.73	H-Bond (Protein Donor)	false
O6A	OD2	ASP- 485	3.42	125.95	H-Bond (Protein Donor)	false
S1P	CB	LYS- 527	3.88	0	Hydrophobic	false
CEP	CB	GLU- 528	4.06	0	Hydrophobic	false
S1P	CB	THR- 530	4.29	0	Hydrophobic	false
CDP	CE2	TYR- 531	4.12	0	Hydrophobic	false
CEP	CD2	TYR- 531	3.74	0	Hydrophobic	false
C6P	CG	TYR- 531	3.69	0	Hydrophobic	false
C2P	CB	TYR- 531	3.85	0	Hydrophobic	false
C1B	CD	LYS- 532	4.31	0	Hydrophobic	false
CEP	CG	LYS- 532	4.25	0	Hydrophobic	false
O2A	NZ	LYS- 532	2.88	169.1	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 532	2.88	0	Ionic (Protein Cationic)	false
C6P	CZ3	TRP- 541	3.69	0	Hydrophobic	false
N4P	O	LEU- 542	2.9	149.66	H-Bond (Ligand Donor)	false
C2P	CD2	LEU- 542	3.61	0	Hydrophobic	false
S1P	CB	ALA- 547	3.72	0	Hydrophobic	false
O4A	MG	MG- 603	2.25	0	Metal Acceptor	false