Table 3. Statistical analysis of the lowest energy structures obtained in the docking calculations of the different cofactors in the 13G10 and 14H7 antibody structures.
| Antibody | Ligand | Buried surface area (Å2)1 | Score (kJ/mol)2 | ΔG (kJ/mol)2 | Shbond (kJ/mol)2 | Hydrogen bondingInteractions(distances in Å) | Slipo(kJ/mol)2 | Hydrophobic contacts | Sclash(kJ/mol)2 | Clashe (distancesin Å) | Sinternal(kJ/mol)2 | Iron distance(Å)3 |
| 13G10 | Fe(ToCPP) | 119.3 | 41.49 | −49.13 | 3.38 | β-COO−/SerH58 OH (2.95)α1- COO−/AsnH33 ND (3.08)α1- COO−/HisH35 NE (2.68)α1- COO−/GlyH96 NH (3.05)α1- COO−/GlyH100a NH (2.82) | 276.65 | TyrL32, AsnL34, TrpL91,AlaL93, AsnL94, LeuL96,AsnH33, HisH35, ValH50IleH51, TyrH52, AspH56,TyrH57, SerH58, GlyH95,GlyH96, AlaH97, GlyH100a,IleH100b, MetH100c | 3.02 | C38– SerH58HB (1.89)C64– TrpL91H (2.3)C64– TrpL91C (3.1) | 4.62 | 1.62 |
| αα–Fe(DoCPP) | 133.4 | 42.01 | −45.26 | 3.19 | α1- COO−/AsnH33 ND (2.97)α1- COO−/HisH35 NE (2.88)α1- COO−/GlyH96 N (2.87)α1- COO−/GlyH100a N (2.9)α2- COO−/AlaH97 N (3.7) | 248.9 | TyrL32, TrpL91, TyrH52,AsnH33, HisH35, ValH50,IleH51, AspH56, TyrH57,SerH58, GlyH95, GlyH96,AlaH97, GlyH100a, IleH100b | 0.87 | C70– GlyH100aHA(1.97) | 2.38 | 0.83 | |
| αβ–Fe(DoCPP) | 125.87 | 40.51 | −43.79 | 2.67 | α- COO−/AsnH33 ND (3.06)α- COO−/HisH35 NE (2.85)α- COO−/GlyH96 N (2.85)α -COO−/GlyH100a N (2.6) | 251.09 | TyrL32, AsnL34, TrpL91,TyrH52, AsnH33, HisH35,ValH50, IleH51, AspH56,TyrH57, SerH58, GlyH95,GlyH96, AlaH97, GlyH100a,IleH100b | 0.92 | C58(H) – SerH58HB2 (2.15) | 2.36 | 0.74 | |
| Fe(MoCPP) | 126.91 | 42.1 | −43.84 | 2.64 | COO−/AsnH33 ND (3.04)COO−/HisH35 NE (2.67)COO−/GlyH100a N (2.73) | 252.46 | TyrL32, AsnL34, TrpL91,TyrH52, AsnH33, HisH35,ValH50, AspH56, TyrH57,SerH58, GlyH95, GlyH96,AlaH97, GlyH100a, IleH100b | 0.29 | – | 1.46 | 1.75 | |
| 14H7 | Fe(ToCPP) | 101.53 | 31.54 | −35.62 | 3.26 | α1-COO−/TYRH52 OH (2.63)α2-COO−/TYRH32 OH (2.96)α2-COO−/SERH97 OH (2.96)β- COO−/ASNL94 ND (3.05) | 164.57 | TyrL32, TrpL91, AsnL94,TyrH32, AsnH33, HisH35,TyrH52, AsnH54, AspH56,ThrH57, SerH58, GlyH100a,LeuH100b | 0.22 | – | 3.87 | TyrH32 OH (4.5) |
| αα–Fe(DoCPP) | 116.34 | 29.84 | −32.08 | 1.98 | α1-COO−/SERH97 OG (2.58)α2-COO−/TYRH32 OH (2.76) | 170.96 | TyrL32, TrpL91, TyrH32,TyrH52, AspH56, GlyH100a,LeuH100b | 0.12 | – | 2.12 | TyrH32 (4.01) | |
| αβ–Fe(DoCPP) | 102.66 | 29.43 | −31.64 | 1.99 | α–COO−/TYRH32 OH (2.73)α–COO−/SERH97 OG (2.80) | 166.85 | TyrL32, TrpL91, AsnL94,TyrH32, TyrH52, AsnH54,AspH56, ThrH57, SerH58,GlyH100a, LeuH100b | 0.19 | C70– SERH58 OH (2.1) | 2.03 | TyrH32 (4.13) | |
| Fe(MoCPP) | 109.55 | 30.63 | −32.17 | 1.88 | COO−/TYRH52 OH (2.6) | 174.54 | SerL30, TyrL32, TrpL91,TrpL93, TyrH52, SerH97,GlyH100a. | 0.15 | – | 1.4 | TyrL32 OH (2.30) |
1
The buried surface area was obtained by subtracting the molecular surfaces (calculated using the UCSF Chimera environment) of the nonbonded cofactor and of the antibody alone, from that of the complex and by dividing the result by 2.
2
The ChemScore scoring is defined as: Score = −(ΔG+Sclash+Sinternal) where the total free energy change that occurs upon ligand binding ΔG = −5.4800 −3.3400*Shbond −6.0300*Smetal −0.1170*Slipo +2.5600*H(rot). Sinternal is the energy term for the internal rotations of the cofactor, Smetal that for the metal interactions and Hrot that for the frozen rotable bonds.
3
For 13G10, distance between the iron atom in the modeled complex and Mg2+ in the crystal structure. For 14H7, distance to iron.