scPDB - 3i53 entry

Protein Data Bank Entry:

PDB ID : 3i53

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2009-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
ID:	NCSB1_STRCZ
AC:	Q84HC8
Organism:	Streptomyces carzinostaticus
Reign:	Bacteria
TaxID:	1897
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	51.634
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.804	749.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	67.26 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.6001	8.57177	24.1011

Binding mode :

What is Poseview ?

2D View
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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
C4'	CZ2	TRP- 133	4.39	0	Hydrophobic	false
C3'	CH2	TRP- 133	3.89	0	Hydrophobic	false
C2'	CE3	TRP- 133	3.65	0	Hydrophobic	false
C5'	CZ2	TRP- 133	3.52	0	Hydrophobic	false
O3'	OD1	ASP- 200	3.41	127.51	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 200	2.58	148.75	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 200	2.72	165.58	H-Bond (Ligand Donor)	false
N6	OG	SER- 227	3.42	172.42	H-Bond (Ligand Donor)	false
C1'	CE1	PHE- 228	4.48	0	Hydrophobic	false
N1	N	PHE- 228	3.03	154.68	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 228	3.4	0	Aromatic Face/Face	false
N	OG	SER- 242	3.01	162.14	H-Bond (Ligand Donor)	false
CG	CB	ALA- 243	3.27	0	Hydrophobic	false
CG	CG2	VAL- 244	4.22	0	Hydrophobic	false
C4'	CG2	VAL- 244	4.35	0	Hydrophobic	false
O4'	O	HOH- 588	3.24	157.55	H-Bond (Protein Donor)	false