Validation using Enzymes existing in M-CSA

EzMechanism Documentation
M-CSA ID Prediction ID PDB ID Results All Rules Shortest Paths Length | n | Depth Own Rules Shortest Paths Length | n | Depth Other Rules Shortest Paths Length | n | Depth Comments
2 1 1tem See results 5 | 32 | 27 - 342 6 | 28 | 17 - 382 5 | 32 | 27 - 342
7 1 4aj3 See results 4 | 10 | 11 - 73 4 | 6 | 11 - 73 0 | 0 | -
8 1 3c2v See results 7 | 312 | 600 - 615 7 | 4 | 600 - 615 0 | 0 | - Tweaked Model PDB: to put N in the right place (substrate is symmetrical)
9 1 5t8s See results 3 | 2 | 2 3 | 1 | 2 0 | 0 | - Protonated His.
10 1 1mka See results 4 | 1 | 21 4 | 1 | 21 6 | 4 | 26 protonated AspB
15 1 4h0d See results 3 | 2 | 2 3 | 1 | 2 3 | 2 | 2
16 1 4h0d See results 4 | 2 | 5 4 | 1 | 5 9 | 10 | 194 - 335 deprotonated product
17 1 1a9t See results 3 | 1 | 5 3 | 1 | 5 4 | 2 | 67 same molecule involved in two parts of the rule changed tautomerization state of products
21 1 1pj2 See results 4 | 8 | 11 - 344 5 | 2 | 24 - 26 4 | 8 | 11 - 344
23 1 1kia See results 2 | 1 | 1 2 | 1 | 1 2 | 1 | 1 tweak: changed protonation state of substrate
24 1 1nzy See results 5 | 2 | 19 5 | 2 | 19 0 | 0 | - Protonated Asp
26 1 4i9t See results 3 | 20 | 2 - 145 3 | 4 | 2 3 | 20 | 2 - 145 tweak: protonated one of the histidines
28 1 1djy See results 3 | 17 | 2 - 562 3 | 3 | 83 - 562 3 | 14 | 2 tweak: put proton in phosphate in products. R groups to C and fix isotope Model not the best, big distances
29 1 1djp See results 4 | 4 | 57 - 138 5 | 2 | 127 - 138 5 | 529 | 126 - 625 tweak: deprotonated amine and protonated aminoacid to be consistent with M29 in products
31 1 1lce See results 6 | 1 | 446 6 | 1 | 446 0 | 0 | - Changed protonation states of Cys and Asp. works but very large distances throughout (water)
32 1 1fro See results 5 | 4 | 28 - 30 5 | 2 | 28 - 30 5 | 4 | 28 - 30
35 1 1phk See results 3 | 2 | 2 3 | 2 | 2 3 | 2 | 2 protonate substrate in products
36 1 1qq6 See results 4 | 16 | 7 - 9 4 | 2 | 7 - 9 0 | 0 | - protonated one of the waters in the products
38 1 4du6 See results 11 | 132 | 5127 - 7975 11 | 132 | 5127 - 7975 0 | 0 | - 10 steps protonated two his
40 1 2paa See results 2 | 2 | 1 2 | 1 | 1 2 | 2 | 1
43 1 2qfp See results 3 | 2 | 2 3 | 1 | 2 4 | 107 | 13 - 930 his not protonated at the end, active site not recycled. phosphate with two protons
44 1 1ew8 See results 3 | 39 | 2 4 | 2 | 4 3 | 39 | 2 Step 4 is a regeneration step.
48 1 4rht See results 3 | 3 | 2 3 | 3 | 2 0 | 0 | -
50 1 3uwq See results 4 | 2 | 7 4 | 2 | 7 0 | 0 | -
51 1 1os1 See results 3 | 1 | 2 3 | 1 | 2 3 | 1 | 2
52 1 3q94 See results 4 | 1 | 4 4 | 1 | 4 4 | 1 | 4 fixed position of the hydroxide in the products conformation of 3q94 not good, Glu too far away
53 1 2gq3 See results 4 | 4 | 14 - 377 4 | 4 | 14 - 377 0 | 0 | - protonated products
54 1 3m7w See results 9 | 424 | 374 - 8653 10 | 8 | 1261 - 6550 0 | 0 | -
55 1 1gu1 See results 4 | 6 | 7 4 | 1 | 7 0 | 0 | - Fixed protonation of Tyr and Glu
57 1 3a8o See results 5 | 5 | 28 - 177 8 | 16 | 65 - 88 0 | 0 | -
58 1 5o5k See results 3 | 4 | 2 3 | 2 | 2 3 | 2 | 2
60 1 1ne7 See results 9 | 18 | 4063 9 | 18 | 4063 0 | 0 | - 8 steps
61 1 1bjp See results 3 | 1 | 2 3 | 1 | 2 0 | 0 | - fixed 2d drawing of n-terminal proline
65 1 5k7x See results 6 | 13 | 31 - 625 6 | 3 | 31 - 625 0 | 0 | - protonated his and deprotonated substrate
67 1 1pjc See results 5 | 2 | 313 5 | 1 | 313 6 | 3 | 160 changed protonation state substrate
69 1 2qia See results 3 | 1 | 2 3 | 1 | 2 3 | 1 | 2
73 1 1dcp See results 5 | 2 | 21 - 48 5 | 2 | 21 - 48 0 | 0 | - protonated two histidines
74 1 1dam See results 5 | 2 | 41 - 137 5 | 2 | 41 - 137 0 | 0 | -
75 1 12as See results 4 | 5 | 11 4 | 4 | 11 4 | 1 | 11 protonated ammonia
77 1 4ubv See results 5 | 2 | 33 5 | 2 | 33 0 | 0 | -
78 1 3csc See results 4 | 2 | 9 - 67 4 | 2 | 9 - 67 0 | 0 | - protonated products
79 1 1jho See results 2 | 1 | 1 2 | 1 | 1 0 | 0 | - fix aromaticity of substrate and which N binds protonated glu in products
80 1 2x75 See results 4 | 8 | 41 - 222 4 | 1 | 41 0 | 0 | - protonated one of the histidines
81 1 4csm See results 2 | 1 | 1 2 | 1 | 1 2 | 1 | 1
83 1 1l8s See results 2 | 1 | 1 3 | 1 | 2 2 | 1 | 1 protonated products
84 1 1b66 See results 7 | 8 | 5634 8 | 4 | 3992 - 4218 0 | 0 | -
85 1 1ik4 See results 5 | 6 | 113 - 493 5 | 2 | 113 7 | 6 | 91 - 98
86 1 4bg4 See results 3 | 10 | 2 3 | 2 | 2 0 | 0 | - deprotonated cysteine protonated product
87 1 5ol4 See results 5 | 24 | 13 - 282 5 | 8 | 13 - 282 0 | 0 | -
90 1 5utu See results 0 | 0 | - 0 | 0 | - 0 | 0 | - protonated asp137 nad to nad+
91 1 3h5q See results 5 | 5 | 4 - 21 5 | 1 | 4 7 | 26 | 110 - 914
95 1 1fui See results 4 | 23 | 4 - 381 5 | 2 | 92 - 184 4 | 21 | 4 - 23
96 1 1chm See results 5 | 1 | 103 5 | 1 | 103 0 | 0 | - deprotonated product protonated second h2o
97 1 4eg2 See results 5 | 2 | 9 6 | 1 | 26 5 | 2 | 9
98 1 5kob See results 4 | 3 | 3 - 12 4 | 1 | 3 0 | 0 | - changed protonation state of two products
100 1 5jry See results 5 | 2 | 46 6 | 8 | 28 - 30 5 | 2 | 46 deprotonated cys protonated glu protonated water in product (extra proton)

Validation using PDB structures not annotated in M-CSA

EzMechanism Documentation
PDB ID Results Shortest Paths Length | n | Depth Comments
7buy See results 5 | 20 | 20 - 214 https://pubs.acs.org/doi/10.1021/acscatal.0c03420 https://link.springer.com/article/10.1007/s11030-021-10259-7 Finds the main mechanism described in the two references. Also finds an alternative mechanism where the Ser side chain forms a cyclic Oxazolidine intermediate with the scissile bond. This is similar with the M-CSA: 225 entry - Adenosylmethionine decarboxylase
7buy See results 6 | 32 | 54 - 297 Similar to the previous example, but where the products are protonated.
1c0a See results 2 | 1 | 1 https://doi.org/10.1021/acs.jpcb.2c03843
3jwe See results 0 | 0 | -
3hju See results 3 | 7 | 2
5foe See results 3 | 3 | 2
1lw4 See results 0 | 0 | -
5xh3 See results 3 | 4 | 2 Substrate trimmed to not include the aromatic rings
5xh3 See results 0 | 0 | - Similar to previous one but know including a bigger portion of the substrate.