scPDB - 4d2c entry

Protein Data Bank Entry:

PDB ID : 4d2c

Resolution :2.470 Å

Experimental Method : X-ray

Deposition Date : 2014-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Di-or tripeptide:H+ symporter
ID:	Q5M4H8_STRT2
AC:	Q5M4H8
Organism:	Streptococcus thermophilus
Reign:	Bacteria
TaxID:	264199
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	39.335
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.664	745.875

% Hydrophobic	% Polar
48.87	51.13
According to VolSite

Ligand :

HET Code:	ALA_PHE
Formula:	C12H16N2O3
Molecular weight:	236.267 g/mol
DrugBank ID:	-
Buried Surface Area:	65.07 %
Polar Surface area:	96.87 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
23.8189	18.0519	-4.94176

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
OXT	NH1	ARG- 26	3.02	156.88	H-Bond (Protein Donor)	false
CB	CZ	TYR- 30	4.1	0	Hydrophobic	false
OXT	OH	TYR- 30	3.24	164.49	H-Bond (Protein Donor)	false
CB	CZ	TYR- 68	4.14	0	Hydrophobic	false
O	NZ	LYS- 126	2.87	162.53	H-Bond (Protein Donor)	false
O	NZ	LYS- 126	2.87	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 126	3.88	0	Ionic (Protein Cationic)	false
CB	CB	ALA- 159	3.61	0	Hydrophobic	false
N	OD1	ASN- 328	2.5	174.25	H-Bond (Ligand Donor)	false
CB	CB	PRO- 329	3.99	0	Hydrophobic	false
N	OE1	GLU- 400	3.99	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 400	3.78	0	Ionic (Ligand Cationic)	false
CE2	CB	SER- 431	3.91	0	Hydrophobic	false