scPDB - 4wcx entry

Protein Data Bank Entry:

PDB ID : 4wcx

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2014-09-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biotin and thiamin synthesis associated
ID:	D3T7F1_THEIA
AC:	D3T7F1
Organism:	Thermoanaerobacter italicus
Reign:	Bacteria
TaxID:	580331
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.531
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.711	516.375

% Hydrophobic	% Polar
50.33	49.67
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	72.84 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
10.9934	13.5446	51.5922

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
C2'	CE1	TYR- 96	4.28	0	Hydrophobic	false
N6	O	TYR- 96	2.85	139.86	H-Bond (Ligand Donor)	false
CE	CE2	TYR- 99	4.35	0	Hydrophobic	false
N	O	ALA- 134	3.16	138.76	H-Bond (Ligand Donor)	false
CA	CB	ALA- 171	4.39	0	Hydrophobic	false
C2'	CD2	PHE- 192	4.09	0	Hydrophobic	false
O3'	OE1	GLU- 194	3.37	125.26	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 194	3.49	120.94	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 194	2.65	156.2	H-Bond (Ligand Donor)	false
O	NZ	LYS- 210	2.98	168.27	H-Bond (Protein Donor)	false
O	NZ	LYS- 210	2.98	0	Ionic (Protein Cationic)	false
C2'	CD2	LEU- 236	4.27	0	Hydrophobic	false
N6	O	ARG- 273	2.92	174.81	H-Bond (Ligand Donor)	false
N1	N	ARG- 273	3.12	156.46	H-Bond (Protein Donor)	false
CE	CD2	TYR- 341	3.26	0	Hydrophobic	false
C5'	CZ	TYR- 341	4.04	0	Hydrophobic	false
C4'	CE1	TYR- 341	4.21	0	Hydrophobic	false
C1'	CE1	TYR- 341	3.79	0	Hydrophobic	false
O3'	O	HOH- 929	2.86	179.97	H-Bond (Protein Donor)	false