in silico tethering 2 (E. coli TS)

Tethering with dimer of E. coli TS (1f4c.pdb, chain A and B)

download 1f4c.pdb
superimpose to 1hvy-AB.pdb - 1f4c.pdbf
load in pymol, correct bonds of ligand and addH - 1f4c_addH.wat.pdb
protonation with whatif using water from X-ray structure (whatif.sh 1f4c_addh.wat) - 1f4c_addh.wat.wi.sup1hvy-AB.pdb
remove water molecules but keeping sulfate
load 1f4c_addh.wi.sup1hvy-AB.pdb in pymol and save again
(this step is important otherwise GOLD has problems with atom types)
remove ligand and side chain of C146 in monomer A using pymol -1f4c_addh-C146G.wi.sup1hvy-AB.pdb
center Ca-C146: 2341
radius: 30 A / 25 A
linking atom of receptor 1f4c_addh-C146G.wi.sup1hvy-AB.pdb: 2341
linking atom of ligand CID_445503-cys3D.sdf: 43
start GOLD 3.1.1: gold_di1f4cC146G_wi.sulf.conf
WARNING: problems with atom types in mol2
(residue 149 altconf B in both monomers)
output: docking_di1f4cC146G_wi_445503.30A.sdf, docking_di1f4cC146G_wi_445503.25A.sdf
active_atoms.pdb active_atoms.1f4c_addh-C146G.wi.pdb
gold_protein.mol2 gold_protein.1f4c_addh-C146G.wi.mol2

/home/henricsn/LIGHTS/results/docking3_C195/

GoldScore

gold_analysis.sh -xray1 1f4c_CID_445503-cys3D.pdb -file docking_di1f4cC146G_wi_445503.30A.sdf

# res RMSD Fit  iVDW  iTOR  eVDW  iHB  eHB  covENE ENE iVDWw  eVDWw  iHBw  eHBw  covENEw

1 xray 7.461 -52.8029 1.3877 -8.9663 -33.3779 0.0000 2.6338 -1.9635 1.3877 -8.9663 -45.8945 0.0000 2.6338 -1.9635

2 xray 7.751 -55.1610 3.6121 -6.0645 -41.9256 0.0000 6.4605 -1.5214 3.6121 -6.0645 -57.6477 0.0000 6.4605 -1.5214

3 xray 5.977 -62.0055 2.8160 -8.8070 -43.9106 0.0000 6.0000 -1.6375 2.8160 -8.8070 -60.3771 0.0000 6.0000 -1.6375

4 xray 2.319 -62.4757 1.9056 -7.3438 -40.2310 0.0000 1.6050 -3.3250 1.9056 -7.3438 -55.3176 0.0000 1.6050 -3.3250

5 xray 5.737 -64.6122 2.5092 -8.1053 -46.8352 0.0000 6.9205 -1.5382 2.5092 -8.1053 -64.3983 0.0000 6.9205 -1.5382

6 xray 5.896 -64.6981 4.5293 -5.8120 -45.6071 0.0000 4.2568 -4.9625 4.5293 -5.8120 -62.7098 0.0000 4.2568 -4.9625

7 xray 8.091 -65.9271 -0.1391 -10.8089 -40.4048 0.0000 4.0080 -3.4304 -0.1391 -10.8089 -55.5566 0.0000 4.0080 -3.4304

8 xray 7.932 -67.5622 -0.9158 -6.5019 -41.8464 0.0000 0.0000 -2.6056 -0.9158 -6.5019 -57.5388 0.0000 0.0000 -2.6056

9 xray 1.685 -67.8001 -2.9336 -8.0178 -39.2537 0.0000 1.4241 -4.2991 -2.9336 -8.0178 -53.9738 0.0000 1.4241 -4.2991

10 xray 5.816 -67.9158 2.7487 -9.4339 -45.0224 0.0000 6.0000 -5.3247 2.7487 -9.4339 -61.9057 0.0000 6.0000 -5.3247



gold_analysis.sh -xray1 1f4c_CID_445503-cys3D.pdb -file docking_di1f4cC146G_wi_445503.25A.sdf

# res RMSD Fit iVDW iTOR eVDW iHB eHB covENE ENE iVDWw eVDWw iHBw eHBw covENEw

1 xray 7.059 -53.6554 1.5339 -9.8560 -35.7038 0.0000 4.6453 -0.8859 1.5339 -9.8560 -49.0927 0.0000 4.6453 -0.8859

2 xray 6.174 -56.9775 1.8227 -9.1005 -39.4056 0.0000 10.8901 -6.4071 1.8227 -9.1005 -54.1827 0.0000 10.8901 -6.4071

3 xray 7.920 -57.9496 1.8692 -6.1964 -41.3819 0.0000 5.6859 -2.4081 1.8692 -6.1964 -56.9002 0.0000 5.6859 -2.4081

4 xray 7.630 -57.9995 3.4108 -6.3219 -45.3283 0.0000 8.5246 -1.2867 3.4108 -6.3219 -62.3264 0.0000 8.5246 -1.2867

5 xray 7.727 -58.1125 2.5235 -7.1572 -43.2214 0.0000 8.1371 -2.1864 2.5235 -7.1572 -59.4295 0.0000 8.1371 -2.1864

6 xray 7.218 -59.4106 1.8865 -6.5564 -42.4627 0.0000 7.6942 -4.0487 1.8865 -6.5564 -58.3862 0.0000 7.6942 -4.0487

7 xray 6.264 -59.6200 1.7308 -9.3865 -40.3900 0.0000 10.8828 -7.3107 1.7308 -9.3865 -55.5363 0.0000 10.8828 -7.3107

8 xray 6.710 -59.9203 3.3641 -6.8164 -40.1840 0.0000 0.0000 -1.2150 3.3641 -6.8164 -55.2531 0.0000 0.0000 -1.2150

9 xray 7.290 -60.5267 0.9452 -8.2531 -43.1196 0.0000 7.9218 -1.8512 0.9452 -8.2531 -59.2894 0.0000 7.9218 -1.8512

10 xray 7.970 -61.8288 3.3481 -7.1348 -40.7716 0.0000 0.0000 -1.9811 3.3481 -7.1348 -56.0609 0.0000 0.0000 -1.9811

11 xray 5.847 -62.3506 2.5914 -6.3487 -45.5108 0.0000 6.0000 -2.0159 2.5914 -6.3487 -62.5774 0.0000 6.0000 -2.0159

12 xray 7.460 -62.4368 2.0702 -7.3273 -44.3348 0.0000 7.6917 -3.9112 2.0702 -7.3273 -60.9604 0.0000 7.6917 -3.9112

13 xray 7.603 -62.6068 0.0594 -9.8903 -41.9610 0.0000 8.1128 -3.1925 0.0594 -9.8903 -57.6963 0.0000 8.1128 -3.1925

14 xray 7.201 -63.0422 1.1815 -10.8683 -38.0361 0.0000 0.4769 -1.5327 1.1815 -10.8683 -52.2996 0.0000 0.4769 -1.5327

15 xray 7.865 -63.6117 1.8420 -7.9624 -40.4864 0.0000 0.0000 -1.8225 1.8420 -7.9624 -55.6687 0.0000 0.0000 -1.8225

16 xray 8.009 -64.0275 1.9998 -6.9127 -46.3081 0.0000 6.0000 -1.4409 1.9998 -6.9127 -63.6736 0.0000 6.0000 -1.4409

17 xray 6.019 -64.1865 2.7110 -7.8456 -46.2650 0.0000 5.9696 -1.4072 2.7110 -7.8456 -63.6144 0.0000 5.9696 -1.4072

18 xray 7.639 -64.2369 1.0763 -7.2250 -45.2230 0.0000 7.5533 -3.4598 1.0763 -7.2250 -62.1816 0.0000 7.5533 -3.4598

19 xray 5.897 -64.3980 2.0160 -8.0546 -45.8951 0.0000 6.0000 -1.2535 2.0160 -8.0546 -63.1057 0.0000 6.0000 -1.2535

20 xray 5.862 -64.7405 2.1562 -7.3402 -46.0626 0.0000 9.0536 -5.2742 2.1562 -7.3402 -63.3360 0.0000 9.0536 -5.2742

21 xray 7.152 -64.7768 0.9766 -6.9280 -44.3109 0.0000 5.3844 -3.2824 0.9766 -6.9280 -60.9274 0.0000 5.3844 -3.2824

22 xray 8.378 -66.0089 -0.8521 -10.8877 -42.9216 0.0000 6.0000 -1.2519 -0.8521 -10.8877 -59.0172 0.0000 6.0000 -1.2519

23 xray 7.478 -66.0980 1.7909 -8.2457 -43.8458 0.0000 2.2773 -1.6325 1.7909 -8.2457 -60.2880 0.0000 2.2773 -1.6325

24 xray 7.802 -66.2510 0.0660 -10.8404 -41.8228 0.0000 8.0972 -6.0675 0.0660 -10.8404 -57.5063 0.0000 8.0972 -6.0675

25 xray 7.912 -66.6104 3.4368 -6.6017 -44.7920 0.0000 0.0000 -1.8565 3.4368 -6.6017 -61.5890 0.0000 0.0000 -1.8565

26 xray 1.864 -67.0297 1.5964 -8.8466 -42.5788 0.0000 1.5566 -2.7901 1.5964 -8.8466 -58.5459 0.0000 1.5566 -2.7901

27 xray 7.279 -67.3864 -1.7611 -10.8591 -44.0698 0.0000 9.1286 -3.2987 -1.7611 -10.8591 -60.5960 0.0000 9.1286 -3.2987

28 xray 7.474 -68.6860 -1.9949 -10.9040 -39.8929 0.0000 0.8371 -1.7715 -1.9949 -10.9040 -54.8528 0.0000 0.8371 -1.7715

29 xray 1.879 -69.2895 2.0592 -8.9155 -45.1306 0.0000 2.2707 -2.6494 2.0592 -8.9155 -62.0545 0.0000 2.2707 -2.6494

30 xray 2.072 -70.2782 1.4384 -10.1420 -44.0764 0.0000 1.1882 -2.1576 1.4384 -10.1420 -60.6051 0.0000 1.1882 -2.1576

ChemScore

gold_analysis.sh -xray1 1f4c_CID_445503-cys3D.pdb -filedocking_di1f4cC146G_wi_445503.CS25A.sdf

# res RMSD Fit  DG  ZeCo HB MET LIPO iHB DEC    DEI ROT COVA HBw   METw LIPOw   iHBw  DECw DEIw ROTw

1 xray 1.138 27.6994 -27.3458 -5.4800 0.8857 0.0000 196.3678 0.0000 -4.6789 3.9731 1.5889 0.3522 -2.9584 -0.0000 -22.9750 0.0000 -4.6789 3.9731 4.0676

2 xray 1.109 27.3465 -27.1459 -5.4800 0.9093 0.0000 193.9867 0.0000 -3.4603 2.6876 1.5889 0.5721 -3.0371 -0.0000 -22.6964 0.0000 -3.4603 2.6876 4.0676

3 xray 1.022 27.3066 -27.0921 -5.4800 0.9114 0.0000 193.4677 0.0000 -4.7773 4.2568 1.5889 0.3060 -3.0440 -0.0000 -22.6357 0.0000 -4.7773 4.2568 4.0676

4 xray 0.852 27.1969 -26.7745 -5.4800 0.9740 0.0000 188.9650 0.0000 -4.8790 4.2244 1.5889 0.2322 -3.2532 -0.0000 -22.1089 0.0000 -4.8790 4.2244 4.0676

5 xray 1.907 27.1308 -26.2075 -5.4800 0.9314 0.0000 185.3351 0.0000 -4.4054 3.3320 1.5889 0.1501 -3.1109 -0.0000 -21.6842 0.0000 -4.4054 3.3320 4.0676

6 xray 1.476 26.9405 -26.8149 -5.4800 0.9166 0.0000 190.9489 0.0000 -4.2146 3.8895 1.5889 0.1995 -3.0615 -0.0000 -22.3410 0.0000 -4.2146 3.8895 4.0676

7 xray 0.739 26.8868 -27.2020 -5.4800 0.9672 0.0000 192.8125 0.0000 -4.3175 3.8010 1.5889 0.8317 -3.2305 -0.0000 -22.5591 0.0000 -4.3175 3.8010 4.0676

8 xray 1.689 26.8388 -27.4677 -5.4800 0.9994 0.0000 194.1659 0.0000 -3.4353 3.7860 1.5889 0.2783 -3.3379 -0.0000 -22.7174 0.0000 -3.4353 3.7860 4.0676

9 xray 1.480 26.8052 -26.8447 -5.4800 0.8529 0.0000 193.0232 0.0000 -4.6538 4.4065 1.5889 0.2868 -2.8486 -0.0000 -22.5837 0.0000 -4.6538 4.4065 4.0676

10 xray 1.738 26.7164 -26.2756 -5.4800 0.9201 0.0000 186.2391 0.0000 -4.4848 3.8354 1.5889 0.2086 -3.0732 -0.0000 -21.7900 0.0000 -4.4848 3.8354 4.0676

11 xray 2.263 26.6578 -25.4879 -5.4800 0.5748 0.0000 189.3655 0.0000 -3.9340 2.4427 1.5889 0.3214 -1.9198 -0.0000 -22.1558 0.0000 -3.9340 2.4427 4.0676

12 xray 2.635 26.5465 -24.9895 -5.4800 0.9443 0.0000 174.5569 0.0000 -4.8861 2.9045 1.5889 0.4245 -3.1539 -0.0000 -20.4232 0.0000 -4.8861 2.9045 4.0676

13 xray 2.085 26.5039 -24.7343 -5.4800 0.6248 0.0000 181.4954 0.0000 -4.6125 2.7629 1.5889 0.0800 -2.0869 -0.0000 -21.2350 0.0000 -4.6125 2.7629 4.0676

14 xray 2.097 26.4827 -25.9045 -5.4800 0.9604 0.0000 181.9158 0.0000 -4.4133 3.4866 1.5889 0.3485 -3.2079 -0.0000 -21.2842 0.0000 -4.4133 3.4866 4.0676

15 xray 2.081 26.3496 -25.3837 -5.4800 0.0000 0.0000 204.8829 0.0000 -4.4426 3.1219 1.5889 0.3548 -0.0000 -0.0000 -23.9713 0.0000 -4.4426 3.1219 4.0676

16 xray 2.091 26.2885 -25.9642 -5.4800 0.9632 0.0000 182.3483 0.0000 -4.3820 3.4423 1.5889 0.6154 -3.2171 -0.0000 -21.3348 0.0000 -4.3820 3.4423 4.0676

17 xray 1.465 26.2667 -26.3181 -5.4800 0.9783 0.0000 184.9423 0.0000 -4.6581 4.6175 1.5889 0.0920 -3.2675 -0.0000 -21.6383 0.0000 -4.6581 4.6175 4.0676

18 xray 2.303 26.2346 -25.3845 -5.4800 0.4892 0.0000 190.9236 0.0000 -4.7789 2.9042 1.5889 1.0245 -1.6340 -0.0000 -22.3381 0.0000 -4.7789 2.9042 4.0676

19 xray 1.153 26.1703 -26.5354 -5.4800 0.8752 0.0000 189.7422 0.0000 -4.4228 3.9962 1.5889 0.7918 -2.9231 -0.0000 -22.1998 0.0000 -4.4228 3.9962 4.0676

20 xray 2.419 26.1537 -25.0148 -5.4800 0.9444 0.0000 174.7707 0.0000 -4.6914 3.2598 1.5889 0.2927 -3.1542 -0.0000 -20.4482 0.0000 -4.6914 3.2598 4.0676

21 xray 1.659 26.0432 -26.7596 -5.4800 0.8838 0.0000 191.4121 0.0000 -2.6342 3.1612 1.5889 0.1895 -2.9520 -0.0000 -22.3952 0.0000 -2.6342 3.1612 4.0676

22 xray 2.023 25.9725 -25.1411 -5.4800 0.0715 0.0000 200.7682 0.0000 -3.3763 2.3758 1.5889 0.1690 -0.2388 -0.0000 -23.4899 0.0000 -3.3763 2.3758 4.0676

23 xray 1.496 25.7777 -26.6370 -5.4800 0.9607 0.0000 188.1686 0.0000 -4.6578 5.3275 1.5889 0.1897 -3.2089 -0.0000 -22.0157 0.0000 -4.6578 5.3275 4.0676

24 xray 1.878 25.6414 -23.5777 -5.4800 0.8762 0.0000 164.4349 0.0000 -4.8992 2.6208 1.5889 0.2146 -2.9264 -0.0000 -19.2389 0.0000 -4.8992 2.6208 4.0676

25 xray 2.734 25.6172 -24.5308 -5.4800 0.9978 0.0000 169.1077 0.0000 -4.4889 3.1305 1.5889 0.2720 -3.3327 -0.0000 -19.7856 0.0000 -4.4889 3.1305 4.0676

26 xray 2.518 25.2803 -25.6364 -5.4800 0.9119 0.0000 181.0103 0.0000 -4.4149 4.5769 1.5889 0.1942 -3.0458 -0.0000 -21.1782 0.0000 -4.4149 4.5769 4.0676

27 xray 4.530 25.1893 -24.9467 -5.4800 0.9999 0.0000 172.6051 0.0000 -4.4999 3.4965 1.5889 0.7609 -3.3395 -0.0000 -20.1948 0.0000 -4.4999 3.4965 4.0676

28 xray 2.661 25.1337 -24.4828 -5.4800 0.9430 0.0000 170.2629 0.0000 -4.7727 3.5107 1.5889 0.6111 -3.1496 -0.0000 -19.9208 0.0000 -4.7727 3.5107 4.0676

29 xray 1.907 25.0721 -24.1643 -5.4800 0.0000 0.0000 194.4606 0.0000 -4.7478 3.5303 1.5889 0.3096 -0.0000 -0.0000 -22.7519 0.0000 -4.7478 3.5303 4.0676

30 xray 1.419 24.7920 -24.4506 -5.4800 0.0256 0.0000 196.1773 0.0000 -4.1327 3.7621 1.5889 0.0291 -0.0855 -0.0000 -22.9527 0.0000 -4.1327 3.7621 4.0676

The last residues Ala263-Ile264 are missing or not defined in 1f4c. Even with using the dimer and sulfates, the docked ligands were directed to the C-terminus and differes from the conformation in the X-ray structure.

SH 23.04.2007

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