Table 1. Retrospective Assessment of HAD Substrate Prediction.
| enrichmenta | examples of correctly predicted
substrates (docking rank)b |
|||
|---|---|---|---|---|
| PDB | good | poor | good | poor |
| 2b82c | 3.30 | 1.98 | IMP (17) | GMP (10) |
| dUMP (16) | ||||
| 4dcc | 3.30 | 1.89 | riboflavin-5-phosphate-(FMN) (9) | l-sorbose-1-phosphate (5) |
| d-iditol-6-phosphate (11) | ||||
| arabinose-5-phosphate (19) | ||||
| 4dfd | 3.30 | 1.89 | riboflavin-5-phosphate-(FMN) (4) | l-sorbose-1-phosphate (9) |
| d-allitol-3-phosphate(15) | ||||
| d-galactitol-6-phosphate(17) | ||||
| 3d6j | 3.30 | 2.50 | d-tagatose-6-phosphate (4) | arabinose-5-phosphate (1) |
| 2-deoxyribose-5-phosphate (5) | d-ribose-5-phosphate(10) | |||
| d-2-deoxy-ribitol-5-phosphate (6) | erythrose-4-phosphate (13) | |||
| 1nrw | 2.93 | 2.16 | isoerythritol-4-phosphate (7) | O-phosphorylethanolamine (3) |
| 2-deoxyribose-5-phosphate (18) | d-ribulose-5-phosphate (4) | |||
| glycerol-3-phosphate (19) | d-threitol-4-phosphate (5) | |||
| ribitol-5-phosphate (20) | glycerol-phosphate-(GP) (6) | |||
| 1rku | 2.40 | 0.60 | O-phospho-l-serine (7) | arabinose-5-phosphate (16) |
| 1te2 | 2.10 | 2.15 | mannose-6-phosphate (11) | glucosamine-6-phosphate (2) |
| ribitol-5-phosphate (14) | d-2-keto-glucose-6-phosphate (5) | |||
| 2-deoxy-d-glucose-6-phosphate (18) | l-ribitol-5-P (6) | |||
| 3pgv(AC) | 1.55 | 1.52 | glucosamine-6-phosphate (2) | allose-6-phosphate (8) |
| d-sedoheptulose-7-phosphate (6) | IMP (9) | |||
| d-psicose-6-phosphate (13) | dGMP (12) | |||
| CMP (20) | d-allitol-6-phosphate (14) | |||
| 4eek | 1.20 | 1.13 | UMP (6) | d-altronate-6-phosphate (14) |
| d-allonate-6-phosphate (12) | CMP (16) | |||
| d-allitol-6-phosphate (17) | ||||
| 3r4c | 1.20 | 0.83 | dAMP (20) | CMP (7) |
| UMP (10) | ||||
| arabinose-5-phosphate (17) | ||||
| 3n07(B) | 1.20 | 0.27 | d-fructose-1,6-bisphosphate (17) | |
| 3niw | 0.80 | 0.44 | arabinose-5-phosphate (7) | mannose-6-phosphate (11) |
| 2obb | 0.00 | 2.20 | dl-glyceraldehyde-3-phosphate (16) | |
| 2hx1 | 0.00 | 1.47 | d-3-deoxy-glucose-6-phosphate (14) | |
| mannitol-6-phosphate (17) | ||||
| 3gygd | 0.00 | 1.47 | dl-glyceraldehyde-3-phosphate (3) | |
| d-ribulose-5-phosphate (7) | ||||
| l-sorbose-1-phosphate (9) | ||||
| 3s6j | 0.00 | 1.44 | erythrose-4-phosphate (2) | |
| dl-glyceraldehyde-3-phosphate (3) | ||||
| arabinose-5-phosphate (6) | ||||
| 3mmzd | 0.00 | 0.69 | d-fructose-1,6-bisphosphate (2) | |
| 6-phosphogluconic-acid (5) | ||||
| mannose-6-phosphate (14) | ||||
| 3n1ud | 0.00 | 0.65 | 6-phosphogluconic-acid (4) | |
| α-d-glucose-1,6-bisphosphate (13) | ||||
| arabinose-5-phosphate (14) | ||||
| 1z5g | 0.00 | 0.00 | ||
| 3ddh(B) | 0.00 | 0.00 | ||
a
Docking enrichment calculated separately for good and poor substrates as defined in the text. An enrichment value of 1 corresponds to random prediction. Values larger than 1 indicate successful docking predictions.
b
Examples of predicted substrates (docking rank indicated in parentheses) that were empirically shown to serve as good or poor substrates for the indicated enzyme.
c
Unless indicated otherwise chain A was used for prediction.
d
Crystallographic symmetry was applied to model the “biological” binding site.