Intercalate Docking Dataset

PDBID DNA Seq. Intercalation site(s) RCSB DNA MD DNA
(5'-3') 1 2 RMSD of top pose(Å) Best RMSD (among 10 poses) (Å) RMSD of top pose(Å) Best RMSD (among 10 poses) (Å)
3FT63FT6120.10.1 (1)1.71.4 (4)
224D224D150.10.1 (1)1.21.2 (1)
282D282D150.20.1 (2)11.0 (1)
258D258D3-0.20.1 (2)1.31.2 (8)
1K9G1K9G150.30.2 (2)1.51.5 (1)
2DES2DES150.20.1 (1)3.81.5 (4)
1IMS1IMS153.10.7 (5)1.31.2 (6)
1IMR1IMR150.20.1 (3)1.31.2 (4)
276D276D1530.4 (2)1.11.1 (5)
1D151D15150.30.3 (1)1.21.1 (2)
482D482D150.10.1 (1)3.43.4 (1)
1D381D38150.40.4 (1)1.21.2 (2)
1D121D12150.50.4 (1)1.21.1 (2)
1NAB1NAB150.30.3 (1)1.61.6 (1)
110D110D150.20.2 (1)1.51.5 (1)
1Z3F1Z3F150.50.1 (6)1.41.4 (8)
1KCI1KCI1520.2 (10)2.41.2 (2)
152D152D151.91.8 (1)1.51.5 (9)
1D101D10151.90.3 (3)1.21.2 (4)
1D371D37150.50.3 (5)2.21.4 (8)
1D541D54150.20.1 (3)3.21.2 (4)
1D581D58150.40.1 (3)1.21.1 (2)
1D671D67150.10.1 (1)1.21.1 (6)
1DA91DA9150.10.1 (1)1.41.3 (2)
1N371N37150.20.2 (1)41.8 (8)
1P201P204-0.30.3 (1)1.31.3 (1)
1QCH1QCH150.20.1 (2)1.21.1 (3)
1R681R682-0.20.1 (6)3.73.7 (1)
215D215D150.50.4 (3)31.1 (2)
234D234D150.10.1 (1)3.53.0 (5)
2GB92GB91520.1 (10)1.41.4 (2)
385D385D153.23.0 (5)3.23.2 (1)
386D386D150.30.1 (2)21.9 (6)
465D465D151.50.1 (9)21.2 (2)
235D235D153.40.3 (2)3.11.4 (4)
236D236D150.40.4 (1)33.0 (2)
245D245D150.10.1 (1)1.21.2 (1)
182D182D150.10.1 (2)1.21.2 (1)
198D198D150.20.2 (1)1.41.3 (4)
151D151D151.81.8 (1)1.31.2 (2)
1DA01DA0152.82.7 (6)1.21.2 (3)
1D111D11150.30.3 (1)1.21.1 (8)
2GJB2GJB150.20.2 (3)0.80.8 (1)
452D452D150.10.1 (3)2.21.4 (6)
1DL81DL8151.51.4 (10)1.81.4 (2)
288D288D153.10.4 (9)1.11.1 (1)
1MNV1MNV360.40.3 (2)5.85.5 (4)
1M691M69150.20.1 (9)2.11.2 (9)
1D361D36150.30.1 (2)1.21.1 (2)
1G3X1G3X150.10.1 (1)4.84.8 (1)
1VTH1VTH150.30.2 (4)1.21.2 (1)
1VTI1VTI150.40.3 (9)32.9 (2)
1JHI1JHI152.52.5 (1)2.91.3 (6)
1DSD1DSD3-0.50.4 (3)5.35.2 (4)
1FJA1FJA4-6.10.4 (4)6.96.6 (2)
1AGL1AGL240.30.1 (3)33.0 (1)
4L5K4L5K150.70.7 (8)22.0 (1)
1D141D14151.81.7 (3)--
1D171D17150.20.2 (3)--
1D221D22152.60.2 (3)--
366D366D151.70.1 (3)--
278D278D1521.8 (3)--
1D211D21150.20.2 (1)--
308D308D152.90.5 (10)--
367D367D151.70.2 (3)--

Intercalate Scoring Dataset

PDB ID Name DNA seq (5'-3') Ligand Ligand charge Binding Energies(kcal/mol)
ΔG° pred ΔG° exp
3FT6proflavineCGATCGProflavine0-6.92-7.1
152DdaunoCGATCGDaunomycin1-9.55-10.1
198DidarubicinCGATCGIdarubicin1-8.95-7.85
1D12doxoCGATCGDoxorubicin1-9.56-9.9
1Z3FellipticineCGATCG Ellipticine1-7.88-7.52
182DnogalamycinTGATCANogalamycin1-9.63-9.3
-san_CGCGCGCGCGCGSanguinarine1-8.51-9.46
-san_ATATATATATATSanguinarine1-8.42-9.36
-PrOPCCGATCGPropyl-OPC (PrOPC )1-8.28-8.93
-MeOPCCGATCGMethyl-OPC (MeOPC )1-8.1-8.82
-HOPCCGATCGOxazolopyridocarbazole chromophore (HOPC )1-8.76-9.05
-coral_GCGCGCGCGCGCCoralyne1-9.6-10.56
-chel_CGCGCGCGCGCGChelerythrine1-8.58-8.57
-EtOPCCGATCGEthyl-OPC (EtOPC )1-8.76-8.773
-quina_CGCGCGCGCGCGQuinacrine2-7.86-9.05
-quina_TATATATATATAQuinacrine2-7.98-8.86
-harma_ATATATATATATHarmalol1-7.3-7.74
-harma_AAAAAAAAAAAAHarmalol1-7.04-7.51
-EB_GGGGGGGGGGGGEthidium Bromide1-7.86-7.98
-thio_ATATATATATATThionine1-7.01-6.95
-psf_GCGCGCGCGCGCPhenosafranine1-7.63-7.54
-psf_ATATATATATATPhenosafranine1-7.26-7.23
-EB_AAAAAAAAAAAAEthidium Bromide1-7.55-7.78
-harma_GGGGGGGGGGGGHarmalol1-6.9-7.33
-psf_GGGGGGGGGGGGPhenosafranine1-7.5-7.48
-saf_GGGGGGGGGGGGSafranine-O1-7.6-7.17
-quina_GGGGGGGGGGGGQuinacrine2-7.75-8.16
-MB_CGCGCGCGCGCGMethylene Blue1-8.41-8.19
-coral_GGGGGGGGGGGGCoralyne1-8.83-8.8
-NMECGATCG2-N methyl ellipticinium (NME)1-8.33-8.37
-9MeECGATCG9-methoxy ellipticine (9meE)0-8.17-8.22
-saf_GCGCGCGCGCGCSafranine-O1-7.49-7.35
-quina_AAAAAAAAAAAAQuinacrine2-8.04-8.14
-MB_AAAAAAAAAAAAMethylene Blue1-7.82-7.56
-saf_ATATATATATATSafranine-O1-7.41-7.05
-san_GGGGGGGGGGGGSanguinarine1-8.28-7.9
-chel_AAAAAAAAAAAAChelerythrine1-8.52-8.24
-mtxCTCGAGMitoxantrone0-8.75-8.38
-9ddCGATCG9-deoxydoxorubicin1-8.51-8.8
-thio_GCGCGCGCGCGCThionine1-7.39-7.9
-thio_GGGGGGGGGGGGThionine1-7.02-7.74
-adron_CGCGATCGAdriamycinone0-7.2-6.3
-san_AAAAAAAAAAAASanguinarine1-8.54-7.9