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. Author manuscript; available in PMC: 2016 Mar 1.
Published in final edited form as: J Struct Funct Genomics. 2015 Jan 29;16(1):43–54. doi: 10.1007/s10969-015-9194-5

Table 2.

ProMOL assigned functions to structures for which BLAST, Pfam, and Dali did not suggest an assignment. There were fifteen instances in which ProMOL suggested a function for a structure, while the other three programs did not. RMSD values were calculated for all non-hydrogen atoms. Fourteen of fifteen alignments in ProMOL consisted of identical active site residue matches between the query and the motif template.

Query ID Motif ID EC Number of Motif RMSD: All (Å) Function Assigned by ProMol Liganda ΔG (kcal/mol)b Kd (μM)
1OQ1 1E2T 2.3.1.118 1.94 transferase KH2 −5.8 57
2DBI 1BP2 3.1.1.4 2.29 hydrolase 8IN −6.1 34
2G6T 1NAA 1.1.99.18 2.13 oxidoreductase ABL −6.1 34
2GFQ 1D6O 5.2.1.8 2.44 isomerase 1KY −10.2 0.034
2P0O 1K9Z 3.1.3.7 0.93 hydrolase AMP −7.2 5.3
2P0V 1AAM 2.6.1.1 1.96 transferase CBA −6.8 10
2PK7 1PJH 5.3.3.8 1.64 isomerase ADP −5.1 180
2Q4K 1OD1 3.4.23.22 2.08 hydrolase 0EO −6.1 34
2XU2 1BMT 2.1.1.13 1.52 transferase C2F −5.7 67
3D19 1HY3 2.8.2.4 2.02 transferase EST −9.5 0.11
3L6I 1C4X 3.7.1.8 2.14 hydrolase 22J −4.8 305
3M3I 4HOH 3.1.27.3 2.69 hydrolase 2GP −6.7 12
3NLC 1BMT 2.1.1.13 1.54 transferase SAH −7.2 5.3
3RBY 1BK7 3.1.27.1 2.15 hydrolase 5GP −6.5 17
4GHB 1PNO 1.6.1.2 1.75 oxidoreductase NAP −8.1 1.2
a
The abbreviations are the names listed in the PDB for the following ligands:
  • KH2: 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate
  • 8IN: [3-(1-benzyl-3-carbamoylmethyl-2-methyl-1h-indol-5-yloxy)-propyl-]-phosphonic acid
  • ABL: 5-amino-5-deoxy-cellobiono-1,5-lactam
  • 1KY: 6-({(1S,5R)-3-[2-(3,4-dimethoxyphenoxy)ethyl]-2-oxo-3,9-diazabicyclo[3.3.1]non-9-yl}sulfonyl)-1,3-benzothiazol-2(3H)-one
  • AMP: adenosine 5′-monophosphate
  • CBA: N-pyridoxyl-2,3-dhydroxyaspartic acid-5-monophosphate
  • ADP: adenosine 5′-diphosphate
  • 0EO: (2S)-2-[[(3S,4S)-5-cyclohexyl-4-[[(4S,5S)-5-[(2-methylpropan-2-yl)oxycarbonylamino]-4-oxidanyl-6-phenyl-hexanoyl]amino]-3-oxidanyl-pentanoyl]amino]-4-methyl-pentanoic acid
  • C2F: 5-methyl-5,6,7,8-tetrahydrofolic acid
  • EST: estradiol
  • 22J: (3E,5R)-5-fluoro-6-(2-fluorophenyl)-2,6-dioxohex-3-enoic acid
  • 2GP: guanosine-2′-monophosphate
  • SAH: S-adenosyl-L-homocysteine
  • 5GP: guanosine-5′-monophosphate
  • NAP: nicotinamide adenine dinucleotide phosphate
b

The binding energy as computed by Autodock Vina [16] was converted to a dissociation constant with the formula: Kd=exp(−ΔG/(R*T)) [http://autodock.scripps.edu/faqs-help/faq/how-autodock-4-converts-binding-energy-kcal-mol-into-ki]