scPDB - 1vfs entry

Protein Data Bank Entry:

PDB ID : 1vfs

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2004-04-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alanine racemase
ID:	Q65YW7_STRLA
AC:	Q65YW7
Organism:	Streptomyces lavendulae subsp. lavendulae
Reign:	Bacteria
TaxID:	58340
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	76 %
B	24 %

Ligand binding site composition:

B-Factor:	18.303
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.272	644.625

% Hydrophobic	% Polar
41.88	58.12
According to VolSite

Ligand :

HET Code:	DCS
Formula:	C11H15N3O7P
Molecular weight:	332.226 g/mol
DrugBank ID:	DB02038
Buried Surface Area:	83.1 %
Polar Surface area:	170.29 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
29.1636	2.6885	15.4738

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
C5A	CG2	VAL- 36	3.89	0	Hydrophobic	false
O2P	OH	TYR- 42	2.75	142.61	H-Bond (Protein Donor)	false
C2A	CE2	TRP- 84	3.73	0	Hydrophobic	false
O3	NH1	ARG- 136	2.8	142.97	H-Bond (Protein Donor)	false
O	NH2	ARG- 136	2.89	130.88	H-Bond (Protein Donor)	false
C2A	CZ3	TRP- 166	3.77	0	Hydrophobic	false
C2A	CB	HIS- 168	4.49	0	Hydrophobic	false
C5A	CB	ASN- 208	4.47	0	Hydrophobic	false
O1P	N	SER- 209	2.93	139.43	H-Bond (Protein Donor)	false
N1	NE	ARG- 224	2.97	163.95	H-Bond (Protein Donor)	false
N1	NH2	ARG- 224	3.34	138.99	H-Bond (Protein Donor)	false
O1P	N	GLY- 226	2.75	152.91	H-Bond (Protein Donor)	false
O2P	N	LEU- 227	3.03	165.3	H-Bond (Protein Donor)	false
O3P	OH	TYR- 361	2.57	158.91	H-Bond (Protein Donor)	false
O	O	HOH- 516	2.61	154.34	H-Bond (Protein Donor)	false
O3	O	HOH- 532	2.93	156.69	H-Bond (Protein Donor)	false