scPDB - 4j7h entry

Protein Data Bank Entry:

PDB ID : 4j7h

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2013-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	PCZA361.3
ID:	O52793_AMYOR
AC:	O52793
Organism:	Amycolatopsis orientalis
Reign:	Bacteria
TaxID:	31958
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.683
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.401	648.000

% Hydrophobic	% Polar
38.54	61.46
According to VolSite

Ligand :

HET Code:	TRH
Formula:	C16H24N2O15P2
Molecular weight:	546.314 g/mol
DrugBank ID:	DB03723
Buried Surface Area:	64.2 %
Polar Surface area:	276.36 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.4045	-11.0709	16.0127

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
O3'	NH2	ARG- 104	3.14	157.92	H-Bond (Protein Donor)	false
C3'	CH2	TRP- 106	4.41	0	Hydrophobic	false
C2'	CE2	TRP- 106	3.64	0	Hydrophobic	false
C1'	CD2	TRP- 106	4.09	0	Hydrophobic	false
C5A	CB	GLN- 108	3.97	0	Hydrophobic	false
O3	OG	SER- 193	2.68	152.33	H-Bond (Ligand Donor)	false
C2	CB	SER- 193	3.8	0	Hydrophobic	false
C4	CH2	TRP- 194	4.02	0	Hydrophobic	false
C3	CZ2	TRP- 194	3.42	0	Hydrophobic	false
O41	NE1	TRP- 288	3.07	138.26	H-Bond (Protein Donor)	false
C5A	CZ2	TRP- 288	4.19	0	Hydrophobic	false
C1'	CE1	TYR- 302	4.08	0	Hydrophobic	false
C5A	CG	TYR- 302	3.5	0	Hydrophobic	false
C5'	CE1	TYR- 302	4.02	0	Hydrophobic	false
C5A	CE1	PHE- 303	3.99	0	Hydrophobic	false
C6	CG2	VAL- 333	3.66	0	Hydrophobic	false
O4P	NH2	ARG- 351	3.29	135.05	H-Bond (Protein Donor)	false
O2	NE2	GLN- 367	3.03	152.51	H-Bond (Protein Donor)	false
C6	CG	GLN- 367	3.95	0	Hydrophobic	false
O3P	N	THR- 369	2.77	173.76	H-Bond (Protein Donor)	false
O3P	ND2	ASN- 372	2.81	154.54	H-Bond (Protein Donor)	false
O4P	OH	TYR- 373	2.62	166.58	H-Bond (Protein Donor)	false
C5'	CZ	TYR- 373	4.17	0	Hydrophobic	false
O4	O	HOH- 750	2.81	179.93	H-Bond (Protein Donor)	false