scPDB - 4dve entry

Protein Data Bank Entry:

PDB ID : 4dve

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2012-02-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biotin transporter BioY
ID:	BIOY_LACLM
AC:	A2RMJ9
Organism:	Lactococcus lactis subsp. cremoris
Reign:	Bacteria
TaxID:	416870
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.307
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.822	455.625

% Hydrophobic	% Polar
55.56	44.44
According to VolSite

Ligand :

HET Code:	BTN
Formula:	C10H15N2O3S
Molecular weight:	243.303 g/mol
DrugBank ID:	DB00121
Buried Surface Area:	77.89 %
Polar Surface area:	106.55 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
33.1159	-20.1012	42.1399

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
C7	CG1	VAL- 36	3.88	0	Hydrophobic	false
N2	O	PRO- 37	2.93	155.65	H-Bond (Ligand Donor)	false
S1	CD1	ILE- 39	4.04	0	Hydrophobic	false
C7	CD1	ILE- 39	3.75	0	Hydrophobic	false
O3	N	ILE- 39	2.94	168.64	H-Bond (Protein Donor)	false
S1	CB	ASN- 42	4.12	0	Hydrophobic	false
O12	OG	SER- 89	2.7	153.28	H-Bond (Protein Donor)	false
C10	CB	SER- 89	3.75	0	Hydrophobic	false
C8	CB	TYR- 92	4.06	0	Hydrophobic	false
C6	CD1	TYR- 92	3.83	0	Hydrophobic	false
C2	CD1	TYR- 92	3.72	0	Hydrophobic	false
O12	NE	ARG- 93	2.92	126.24	H-Bond (Protein Donor)	false
O12	NH2	ARG- 93	2.57	136.78	H-Bond (Protein Donor)	false
O12	CZ	ARG- 93	3.11	0	Ionic (Protein Cationic)	false
C10	CG	ARG- 93	4.03	0	Hydrophobic	false
C10	CH2	TRP- 96	4.03	0	Hydrophobic	false
C8	CZ2	TRP- 96	4.25	0	Hydrophobic	false
S1	CZ2	TRP- 96	3.86	0	Hydrophobic	false
C6	CG1	VAL- 133	4.22	0	Hydrophobic	false
N1	OD2	ASP- 163	3.12	133.96	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 163	3.02	163.72	H-Bond (Ligand Donor)	false