scPDB - 1yli entry

Protein Data Bank Entry:

PDB ID : 1yli

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2005-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized acyl-CoA thioester hydrolase HI_0827
ID:	Y827_HAEIN
AC:	P44886
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	3.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	60 %
B	40 %

Ligand binding site composition:

B-Factor:	33.126
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.644	536.625

% Hydrophobic	% Polar
36.48	63.52
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	52.62 %
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
-25.8355	-20.9638	8.24846

Binding mode :

What is Poseview ?

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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
O4A	CA	CA- 1	2.37	0	Metal Acceptor	false
S1P	CG1	ILE- 39	4.28	0	Hydrophobic	false
CDP	CG2	VAL- 60	3.98	0	Hydrophobic	false
C6P	CG2	VAL- 60	3.72	0	Hydrophobic	false
N4P	O	THR- 61	2.88	147.06	H-Bond (Ligand Donor)	false
CDP	CG2	VAL- 62	3.8	0	Hydrophobic	false
N6A	OD1	ASN- 68	2.71	133.26	H-Bond (Ligand Donor)	false
N8P	O	PHE- 69	3.02	138.99	H-Bond (Ligand Donor)	false
C6P	CB	PHE- 69	4.47	0	Hydrophobic	false
C2P	CD1	PHE- 69	3.91	0	Hydrophobic	false
OAP	O	ILE- 70	3.44	157.64	H-Bond (Ligand Donor)	false
S1P	CD1	ILE- 73	4.12	0	Hydrophobic	false
O8A	N	ARG- 90	2.76	126.38	H-Bond (Protein Donor)	false
O8A	N	SER- 91	3.14	143.15	H-Bond (Protein Donor)	false
O9A	N	SER- 91	2.79	144.16	H-Bond (Protein Donor)	false
O9A	OG	SER- 91	2.55	173.33	H-Bond (Protein Donor)	false
C1B	CB	SER- 92	4.34	0	Hydrophobic	false
C4B	CB	SER- 92	4.3	0	Hydrophobic	false
O8A	OG	SER- 92	2.56	169.16	H-Bond (Protein Donor)	false
O8A	N	SER- 92	2.99	159.97	H-Bond (Protein Donor)	false
S1P	CG1	VAL- 115	3.92	0	Hydrophobic	false
C4B	CG2	VAL- 123	4.14	0	Hydrophobic	false
C5B	CG1	VAL- 123	3.98	0	Hydrophobic	false
CDP	CG2	VAL- 123	3.97	0	Hydrophobic	false
CEP	CG1	VAL- 125	4.27	0	Hydrophobic	false
C5B	CB	SER- 131	3.8	0	Hydrophobic	false
O2A	OG	SER- 131	2.64	172	H-Bond (Protein Donor)	false
O5P	O	HOH- 183	2.77	159.34	H-Bond (Protein Donor)	false