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1 upplementary Material Molecular docking and ligand specificity in fragmentbased inhibitor discovery Chen & hoichet 26
2 27 (a) (b) (c)
3 igure 1 Inhibitors identified against CTXM. K i values were determined for compounds 14, 6, 11, 12, 13 and 14, the first seven of which were also crystallized. (a) ragment inhibitors identified by molecular docking. All had IC 50 ~mm. Compounds 1, 4, 5 were also previously identified as inhibitors against AmpC. (b) Leadlike tetrazole compounds selected by molecular docking. Their Ki values ranged from mm to submm with the best at 21 μm (compound 12). (c) Analogs of the most potent tetrazole inhibitor from docking, identified by similarity search. All inhibited CTXM at 250 μm and the best has Ki at 10 μm (compound 13). 28
4
5 igure 2 onbinding fragments selected by docking. These compounds did not inhibit CTXM when tested at up to 5 mm concentrations, or as their solubility allowed. 30
6 P Br + P
7 igure 3 onbinding leadlike compounds selected by docking. These compounds did not inhibit CTXM when tested at up to 5 mm concentrations, or as their solubility allowed. 32
8 Table 1 ragment database compounds most similar to ligands # ligand Whole database a uster centers b Random cluster set c structure score d structure score structure score Br Ṉ a. Latest fragment subset of ZIC database, 317,000 compounds. b. The compounds that are the centers of the 2500 clusters from the fragment database. c. The compounds randomly chosen from the 2500 clusters (one from each cluster). d. Tanimoto similarity score between the ligand and the compound using ECP4 fingerprint. 33
9 Table 2 * Values in parenthesis represent highest resolution shells. Crystallographic statistics Compound # Data collection pace group P2 1 P2 1 P322 1 P2 1 P2 1 P2 1 P2 1 Cell dimensions a, b, c (Å) α, β, γ ( ) ( ) ( ) ( ) ( ) ( ) Resolution ( Å) ( )* ( ) R merge (%) 5.1 (21.2) 4.6 (34.5) 5.6 (57.1) 7.7 (34.1) 5.1 (27.1) 4.7 (24.9) 4.4 (30.0) I / σi 11.3(2.9) 15.0 (2.0) 20.7 (2.0) 10.8 (2.4) 20.6 (4.0) 22.6 (5.1) 16.7 (2.6) Completeness(%) 91.6 (96.7) 98.3 (93.5) 99.7 (98.5) 98.6 (87.1) 99.4 (98.3) 99.9 (99.9) 98.6 (94.0) Redundancy 1.8 (1.7) 2.5 (2.0) 7.4 (5.9) 3.5 (2.9) 3.9 (3.7) 3.9 (3.6) 2.5 (2.2) Refinement Resolution (Å) ( ) ( ) ( ) ( ) ( ) ( ) ( ) o. reflections (10197) (6567) (2167) (4241) (10346) (10591) (8057) R work /R free 16.1 / / / / / (18.0) 15.5 / 18.2 o. atoms Protein Ligand/ion Water Bfactors (Å 2 ) Protein Ligand/ion Water r.m.s. deviations bond lengths (Å) bond angles ( )
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