scPDB - 4iil entry

Protein Data Bank Entry:

PDB ID : 4iil

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2012-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Membrane lipoprotein TpN38(b)
ID:	TPN38_TREPA
AC:	Q56328
Organism:	Treponema pallidum
Reign:	Bacteria
TaxID:	243276
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.534
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.925	455.625

% Hydrophobic	% Polar
58.52	41.48
According to VolSite

Ligand :

HET Code:	RBF
Formula:	C17H20N4O6
Molecular weight:	376.364 g/mol
DrugBank ID:	DB00140
Buried Surface Area:	75.44 %
Polar Surface area:	155.04 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
26.7313	40.2247	18.2766

Binding mode :

What is Poseview ?

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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
N3	OG	SER- 24	2.87	153.52	H-Bond (Ligand Donor)	false
C2'	CG2	VAL- 26	3.87	0	Hydrophobic	false
C3'	CG1	VAL- 26	4.13	0	Hydrophobic	false
N5	OH	TYR- 27	3.16	136.42	H-Bond (Protein Donor)	false
C7M	CZ3	TRP- 62	3.97	0	Hydrophobic	false
C9	CB	ASN- 82	4.06	0	Hydrophobic	false
C8M	CG	PRO- 83	3.93	0	Hydrophobic	false
C7M	CB	ALA- 84	3.95	0	Hydrophobic	false
C8M	CB	ALA- 84	4.24	0	Hydrophobic	false
O2'	OD2	ASP- 105	2.98	172.98	H-Bond (Ligand Donor)	false
O5'	NE2	GLN- 121	2.83	154.68	H-Bond (Protein Donor)	false
C8M	CD2	TYR- 157	3.58	0	Hydrophobic	false
C1'	CZ	TYR- 157	4.23	0	Hydrophobic	false
O3'	OH	TYR- 157	2.66	133.69	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 164	3.98	0	Hydrophobic	false
C1'	CH2	TRP- 189	3.49	0	Hydrophobic	false
C9A	CZ2	TRP- 189	3.42	0	Hydrophobic	false
C4'	CG2	ILE- 213	3.58	0	Hydrophobic	false
C5'	CE2	PHE- 235	3.79	0	Hydrophobic	false
O4'	OD2	ASP- 236	2.75	157.88	H-Bond (Ligand Donor)	false
O5'	OD2	ASP- 236	3.34	136.01	H-Bond (Ligand Donor)	false
O5'	OD1	ASP- 236	2.72	163.82	H-Bond (Ligand Donor)	false
O3'	O	HOH- 555	2.59	171.3	H-Bond (Ligand Donor)	false