scPDB - 3r3d entry

Protein Data Bank Entry:

PDB ID : 3r3d

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2011-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxybenzoyl-CoA thioesterase
ID:	4HBT_ARTSP
AC:	Q04416
Organism:	Arthrobacter sp
Reign:	Bacteria
TaxID:	1667
EC Number:	3.1.2.23

Chains:

Chain Name:	Percentage of Residues within binding site
A	54 %
B	46 %

Ligand binding site composition:

B-Factor:	22.671
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.191	776.250

% Hydrophobic	% Polar
56.52	43.48
According to VolSite

Ligand :

HET Code:	4CO
Formula:	C29H38N7O18P3S
Molecular weight:	897.634 g/mol
DrugBank ID:	DB03613
Buried Surface Area:	54.36 %
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:	22

Mass center Coordinates

X	Y	Z
85.6025	26.3422	21.8498

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
C4B	CB	GLN- 58	3.2	0	Hydrophobic	false
C3B	CG	GLN- 58	3.38	0	Hydrophobic	false
C2P	CD1	LEU- 62	4.43	0	Hydrophobic	false
O1B	N	GLY- 65	2.68	159.62	H-Bond (Protein Donor)	false
C2B	CG	GLU- 73	4.32	0	Hydrophobic	false
CB	CG	GLU- 73	4.02	0	Hydrophobic	false
C3B	CB	MET- 74	4.3	0	Hydrophobic	false
C4B	CG	MET- 74	3.59	0	Hydrophobic	false
CB	CB	SER- 77	4.25	0	Hydrophobic	false
C7B	CB	SER- 77	3.42	0	Hydrophobic	false
O2B	OE2	GLU- 78	2.6	166.73	H-Bond (Ligand Donor)	false
C6B	CG	GLU- 78	3.73	0	Hydrophobic	false
CDP	CE	MET- 90	4.41	0	Hydrophobic	false
CDP	CG2	VAL- 92	4.03	0	Hydrophobic	false
CEP	CG2	VAL- 92	3.95	0	Hydrophobic	false
C6P	CG2	VAL- 92	3.76	0	Hydrophobic	false
S1P	CB	VAL- 92	3.76	0	Hydrophobic	false
N4P	O	GLY- 93	3.2	159.12	H-Bond (Ligand Donor)	false
CEP	CB	GLN- 94	4.11	0	Hydrophobic	false
N8P	O	PHE- 100	3.31	158.85	H-Bond (Ligand Donor)	false
C6P	CB	PHE- 100	3.84	0	Hydrophobic	false
O3D	NH1	ARG- 102	3.1	126.6	H-Bond (Protein Donor)	false
C1D	CG	PRO- 103	4.14	0	Hydrophobic	false
CDP	CB	ALA- 145	4.41	0	Hydrophobic	false
CEP	CB	ALA- 145	3.8	0	Hydrophobic	false
CDP	CG	ARG- 147	4.27	0	Hydrophobic	false
N6A	O	PRO- 148	2.97	160.93	H-Bond (Ligand Donor)	false
O7A	CZ	ARG- 150	3.67	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 150	3.6	0	Ionic (Protein Cationic)	false
O7A	NH1	ARG- 150	2.73	170.36	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 150	2.77	174.29	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 150	3.88	164.13	Pi/Cation	false
O5P	O	HOH- 501	2.84	152.95	H-Bond (Protein Donor)	false
O2B	O	HOH- 523	2.96	179.97	H-Bond (Protein Donor)	false