scPDB - 3i5x entry

Protein Data Bank Entry:

PDB ID : 3i5x

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-07-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent RNA helicase MSS116, mitochondrial
ID:	MS116_YEAST
AC:	P15424
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	3.6.4.13

Chains:

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

Ligand binding site composition:

B-Factor:	14.876
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.639	567.000

% Hydrophobic	% Polar
48.81	51.19
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	67.24 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
66.3365	33.6875	16.6833

Binding mode :

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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
C1'	CE1	PHE- 126	4.39	0	Hydrophobic	false
N6	O	GLY- 128	2.85	166.65	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 133	2.87	167.11	H-Bond (Protein Donor)	false
N6	OE1	GLN- 133	2.99	140.49	H-Bond (Ligand Donor)	false
O2B	N	THR- 156	3.25	136.2	H-Bond (Protein Donor)	false
O3A	N	GLY- 157	3.35	149.78	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 158	2.71	168.48	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 158	2.72	148.44	H-Bond (Protein Donor)	false
O2B	N	LYS- 158	3.07	168.38	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 158	2.71	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 158	3.98	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 158	2.72	0	Ionic (Protein Cationic)	false
O1A	OG1	THR- 159	2.76	153.2	H-Bond (Protein Donor)	false
O1A	N	THR- 159	2.98	157.35	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 441	2.69	148.25	H-Bond (Ligand Donor)	false
O2G	CZ	ARG- 466	3.26	0	Ionic (Protein Cationic)	false
O2G	NH2	ARG- 466	2.85	142.04	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 466	2.81	143.87	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 469	2.74	157.14	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 469	3.29	130.35	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 469	3.03	120.51	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 469	3.44	0	Ionic (Protein Cationic)	false
C4'	CB	SER- 470	4.05	0	Hydrophobic	false
C1'	CB	SER- 470	4.24	0	Hydrophobic	false
O3G	MG	MG- 900	1.95	0	Metal Acceptor	false
O1B	MG	MG- 900	1.95	0	Metal Acceptor	false
O1G	O	HOH- 1051	2.83	179.97	H-Bond (Protein Donor)	false
O2'	O	HOH- 1087	2.62	163.56	H-Bond (Protein Donor)	false