scPDB - 5kgp entry

Protein Data Bank Entry:

PDB ID : 5kgp

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2016-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Predicted acetyltransferase
ID:	Q97ML2_CLOAB
AC:	Q97ML2
Organism:	Clostridium acetobutylicum
Reign:	Bacteria
TaxID:	272562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	13.355
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	840.375

% Hydrophobic	% Polar
51.81	48.19
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	61.48 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
10.0321	-4.63708	-17.6249

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
C6P	CG2	ILE- 20	4.3	0	Hydrophobic	false
CH3	CG2	ILE- 78	4.21	0	Hydrophobic	false
CDP	CG1	ILE- 81	4.22	0	Hydrophobic	false
N4P	O	ILE- 81	2.81	166.97	H-Bond (Ligand Donor)	false
O	N	ILE- 81	3.22	126.06	H-Bond (Protein Donor)	false
C6P	CG2	ILE- 82	4.24	0	Hydrophobic	false
CDP	CG2	VAL- 83	4.1	0	Hydrophobic	false
CAP	CB	VAL- 83	4.43	0	Hydrophobic	false
O9P	N	VAL- 83	2.78	160.85	H-Bond (Protein Donor)	false
CAP	CD	ARG- 88	3.51	0	Hydrophobic	false
O5A	N	HIS- 89	2.86	166.02	H-Bond (Protein Donor)	false
O1A	N	GLY- 91	2.88	147.42	H-Bond (Protein Donor)	false
O4A	N	GLY- 93	2.74	152.6	H-Bond (Protein Donor)	false
O2A	N	THR- 94	2.9	146.37	H-Bond (Protein Donor)	false
O2A	OG1	THR- 94	2.51	157.56	H-Bond (Protein Donor)	false
CH3	CB	CYS- 114	3.98	0	Hydrophobic	false
S1P	CG2	ILE- 125	4.13	0	Hydrophobic	false
C6P	SG	CYS- 129	4.46	0	Hydrophobic	false
C2P	SG	CYS- 129	3.92	0	Hydrophobic	false
CEP	CB	SER- 132	3.78	0	Hydrophobic	false
C1B	CB	PHE- 135	4.08	0	Hydrophobic	false
CCP	CD1	PHE- 135	3.89	0	Hydrophobic	false
CEP	CD2	PHE- 135	4.04	0	Hydrophobic	false
C5B	CD1	PHE- 135	4.07	0	Hydrophobic	false
S1P	CE2	PHE- 136	4.06	0	Hydrophobic	false
CH3	CZ	PHE- 136	4.29	0	Hydrophobic	false
N1A	ND2	ASN- 295	2.99	142.89	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 295	3.2	158.77	H-Bond (Ligand Donor)	false
O4A	O	HOH- 545	2.66	154.39	H-Bond (Protein Donor)	false