scPDB - 3i4l entry

Protein Data Bank Entry:

PDB ID : 3i4l

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-07-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	V-type ATP synthase alpha chain
ID:	VATA_PYRHO
AC:	O57728
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	3.6.3.14

Chains:

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

Ligand binding site composition:

B-Factor:	51.472
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.267	438.750

% Hydrophobic	% Polar
66.92	33.08
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	70.56 %
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
44.7241	10.5455	24.2374

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
O3G	OG	SER- 238	2.53	157.5	H-Bond (Protein Donor)	false
C4'	CG2	THR- 241	3.48	0	Hydrophobic	false
C3'	CB	THR- 241	3.72	0	Hydrophobic	false
C1'	CG2	VAL- 242	3.74	0	Hydrophobic	false
C3'	CG2	THR- 243	3.52	0	Hydrophobic	false
C2'	CB	THR- 243	4.22	0	Hydrophobic	false
C1'	CG2	THR- 243	3.98	0	Hydrophobic	false
C3'	CD1	LEU- 417	4.21	0	Hydrophobic	false
C5'	CB	ALA- 422	3.68	0	Hydrophobic	false
C5'	CE2	PHE- 427	3.65	0	Hydrophobic	false
C1'	CD2	PHE- 427	3.66	0	Hydrophobic	false
C2'	CB	PRO- 428	4.18	0	Hydrophobic	false
O2'	N	ALA- 429	3.02	126.41	H-Bond (Protein Donor)	false
C3'	CB	ALA- 429	3.63	0	Hydrophobic	false
N1	N	ALA- 507	3.04	128.41	H-Bond (Protein Donor)	false