Hi! I’m trying to dock the peptide Cilengitide onto the human avb3 integrin. However, this peptide has a modified valine (cyclo[Arg-Gly-Asp-D-Phe-N(Me)Val]) which isn’t currently in the list of modified amino acids permitted for HADDOCK. Would it be possible to add this modified aa/would you happen to have have a suggested workaround?
(For additional context I’m trying to replicate the crystal structure PDB 1l5g. Cilengitide is also available on PubChem: Cilengitide | C27H40N8O7 | CID 176873 - PubChem )
This is how Cilengitide appears in the 1l5g PDB file (with MVA being the modified aa):
ATOM 11401 N ARG C5001 18.197 44.746 45.046 1.00 34.43 N
ATOM 11402 CA ARG C5001 17.292 45.307 44.062 1.00 28.14 C
ATOM 11403 C ARG C5001 17.823 44.666 42.776 1.00 29.22 C
ATOM 11404 O ARG C5001 19.041 44.617 42.561 1.00 26.11 O
ATOM 11405 CB ARG C5001 17.357 46.833 44.018 1.00 27.48 C
ATOM 11406 CG ARG C5001 16.636 47.514 45.175 1.00 30.15 C
ATOM 11407 CD ARG C5001 16.409 49.004 44.914 1.00 25.58 C
ATOM 11408 NE ARG C5001 15.446 49.245 43.845 1.00 28.89 N
ATOM 11409 CZ ARG C5001 15.302 50.405 43.213 1.00 37.36 C
ATOM 11410 NH1 ARG C5001 16.060 51.444 43.543 1.00 37.45 N
ATOM 11411 NH2 ARG C5001 14.440 50.511 42.205 1.00 41.68 N
ATOM 11412 N GLY C5002 16.915 44.084 41.988 1.00 37.97 N
ATOM 11413 CA GLY C5002 17.294 43.402 40.758 1.00 34.71 C
ATOM 11414 C GLY C5002 17.721 41.984 41.095 1.00 29.22 C
ATOM 11415 O GLY C5002 17.066 41.315 41.891 1.00 31.47 O
ATOM 11416 N ASP C5003 18.817 41.525 40.499 1.00 22.58 N
ATOM 11417 CA ASP C5003 19.341 40.182 40.769 1.00 20.34 C
ATOM 11418 C ASP C5003 20.273 40.270 41.991 1.00 23.10 C
ATOM 11419 O ASP C5003 21.469 39.974 41.902 1.00 23.76 O
ATOM 11420 CB ASP C5003 20.111 39.682 39.544 1.00 15.88 C
ATOM 11421 CG ASP C5003 20.510 38.219 39.648 1.00 20.37 C
ATOM 11422 OD1 ASP C5003 19.790 37.453 40.322 1.00 17.02 O
ATOM 11423 OD2 ASP C5003 21.534 37.835 39.032 1.00 18.58 O
ATOM 11424 N PHE C5004 19.699 40.678 43.127 1.00 25.80 N
ATOM 11425 CA PHE C5004 20.419 40.876 44.392 1.00 37.44 C
ATOM 11426 C PHE C5004 19.454 41.526 45.375 1.00 41.23 C
ATOM 11427 O PHE C5004 18.373 40.988 45.638 1.00 47.66 O
ATOM 11428 CB PHE C5004 20.928 39.550 44.971 1.00 48.16 C
ATOM 11429 CG PHE C5004 21.724 39.695 46.268 1.00 58.10 C
ATOM 11430 CD1 PHE C5004 23.117 39.747 46.247 1.00 59.11 C
ATOM 11431 CD2 PHE C5004 21.078 39.733 47.507 1.00 62.65 C
ATOM 11432 CE1 PHE C5004 23.849 39.833 47.432 1.00 61.44 C
ATOM 11433 CE2 PHE C5004 21.803 39.820 48.694 1.00 63.45 C
ATOM 11434 CZ PHE C5004 23.192 39.869 48.653 1.00 64.02 C
HETATM11435 N MVA C5005 19.819 42.703 45.915 1.00 39.04 N
HETATM11436 CN MVA C5005 20.837 43.469 45.344 1.00 39.28 C
HETATM11437 CA MVA C5005 18.873 43.313 46.867 1.00 39.45 C
HETATM11438 CB MVA C5005 19.587 44.375 47.762 1.00 41.14 C
HETATM11439 CG1 MVA C5005 18.631 44.863 48.855 1.00 37.72 C
HETATM11440 CG2 MVA C5005 20.845 43.777 48.416 1.00 50.20 C
HETATM11441 C MVA C5005 17.774 43.914 45.993 1.00 42.33 C
HETATM11442 O MVA C5005 16.580 43.613 46.159 1.00 44.53 O
TER 11443 MVA C5005