sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 1.386 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 1.259 | |
| 3djk | G55 | Gag-Pol polyprotein | 3.4.23.16 | 1.253 | |
| 2hb3 | GRL | Protease | / | 1.233 | |
| 3vf7 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 1.224 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 1.223 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 1.214 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 1.201 | |
| 3ok9 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 1.190 | |
| 3o9a | K14 | Pol polyprotein | / | 1.175 | |
| 2qci | 065 | Gag-Pol polyprotein | 3.4.23.16 | 1.169 | |
| 4heg | G52 | Gag-Pol polyprotein | 3.4.23.16 | 1.164 | |
| 2i4u | DJR | Protease | / | 1.154 | |
| 4djo | MK5 | Pol polyprotein | / | 1.139 | |
| 4kb9 | G79 | Protease | / | 1.138 | |
| 2z4o | 065 | Gag-Pol polyprotein | 3.4.23.16 | 1.136 | |
| 3pwm | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.117 | |
| 3o9b | K2A | Pol polyprotein | / | 1.116 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 1.115 | |
| 3o9c | K20 | Pol polyprotein | / | 1.111 | |
| 1t3r | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.110 | |
| 2i4d | QFI | Protease | / | 1.108 | |
| 3sa8 | K83 | Protease | / | 1.107 | |
| 3ecg | 065 | Gag-Pol polyprotein | 3.4.23.47 | 1.106 | |
| 3o9f | K2D | Gag-Pol polyprotein | / | 1.106 | |
| 3oy4 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.100 | |
| 3o9d | K19 | Pol polyprotein | / | 1.098 | |
| 2qd6 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 1.097 | |
| 4dqe | 017 | Gag-Pol polyprotein | / | 1.097 | |
| 3o9h | K2E | Gag-Pol polyprotein | / | 1.096 | |
| 3vfb | 031 | Gag-Pol polyprotein | 3.4.23.16 | 1.096 | |
| 4dqb | 017 | Gag-Pol polyprotein | / | 1.096 | |
| 4dqh | 017 | Gag-Pol polyprotein | / | 1.093 | |
| 4dqf | 017 | Gag-Pol polyprotein | / | 1.089 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 1.086 | |
| 2i0a | MUI | Protease | / | 1.075 | |
| 4djq | M86 | Pol polyprotein | / | 1.073 | |
| 3mxd | K53 | Gag-Pol polyprotein | 3.4.23.16 | 1.072 | |
| 3ec0 | GRL | Gag-Pol polyprotein | 3.4.23.47 | 1.070 | |
| 3qaa | G04 | Gag-Pol polyprotein | 3.4.23.16 | 1.065 | |
| 2qi7 | MZ9 | Gag-Pol polyprotein | / | 1.061 | |
| 2i4w | KGQ | Protease | / | 1.059 | |
| 3o9e | A60 | Pol polyprotein | / | 1.056 | |
| 3d20 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.055 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.054 | |
| 4dqc | 017 | Gag-Pol polyprotein | / | 1.054 | |
| 3r4b | 74T | Gag-Pol polyprotein | / | 1.050 | |
| 4njs | G08 | Protease | / | 1.045 | |
| 3saa | 77F | Protease | / | 1.039 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 1.038 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 1.035 | |
| 2i4x | KGQ | Protease | / | 1.032 | |
| 2i4v | DJR | V-1 protease | / | 1.031 | |
| 4hdf | G52 | Gag-Pol polyprotein | 3.4.23.16 | 1.027 | |
| 4djp | M73 | Pol polyprotein | / | 1.023 | |
| 3o99 | K13 | Pol polyprotein | / | 1.021 | |
| 3o9i | A61 | Gag-Pol polyprotein | / | 1.020 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.016 | |
| 2idw | 017 | Protease | / | 1.012 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.009 | |
| 4q1w | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.008 | |
| 3mxe | K54 | Gag-Pol polyprotein | 3.4.23.16 | 1.001 | |
| 3jvy | 017 | Gag-Pol polyprotein | 3.4.23.16 | 1.000 | |
| 2ieo | 017 | Protease | / | 0.998 | |
| 3sa9 | A68 | Protease | / | 0.998 | |
| 4hdb | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.998 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.995 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.993 | |
| 3gi4 | K60 | Gag-Pol polyprotein | / | 0.992 | |
| 3i6o | GR6 | Gag-Pol polyprotein | 3.4.23.16 | 0.992 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.989 | |
| 2psu | MUU | Protease | / | 0.987 | |
| 2qi6 | MZ8 | Gag-Pol polyprotein | / | 0.987 | |
| 3lzv | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.986 | |
| 3sab | F78 | Protease | / | 0.986 | |
| 4q1y | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.986 | |
| 2qi4 | MZ6 | Gag-Pol polyprotein | / | 0.985 | |
| 3gi5 | K62 | Gag-Pol polyprotein | / | 0.984 | |
| 4j54 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.981 | |
| 3ekv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.978 | |
| 2qhy | MZ1 | Gag-Pol polyprotein | / | 0.974 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.974 | |
| 3gi6 | D78 | Gag-Pol polyprotein | / | 0.971 | |
| 3mws | 017 | Pol protein | / | 0.971 | |
| 4djr | 0KJ | Pol polyprotein | / | 0.970 | |
| 4ye3 | G04 | Gag-Pol polyprotein | 3.4.23.16 | 0.970 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.964 | |
| 2qi0 | MZ3 | Gag-Pol polyprotein | / | 0.964 | |
| 2qd8 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.953 | |
| 2i0d | MUT | Protease | / | 0.952 | |
| 2hs1 | 017 | Protease | / | 0.949 | |
| 3d1z | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.945 | |
| 2qhz | MZ2 | Gag-Pol polyprotein | / | 0.944 | |
| 3nu4 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.944 | |
| 3lzu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.943 | |
| 3em6 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.939 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.934 | |
| 3ucb | 017 | Gag-Pol polyprotein | / | 0.923 | |
| 3sa4 | F72 | Protease | / | 0.922 | |
| 3s54 | 017 | Protease | / | 0.917 | |
| 3nuj | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.916 | |
| 3nu9 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.915 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.902 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.899 | |
| 3nu6 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.897 | |
| 2qi5 | MZ7 | Gag-Pol polyprotein | / | 0.895 | |
| 3oxw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.893 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.892 | |
| 4njt | 017 | Protease | / | 0.892 | |
| 4q1x | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.892 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.884 | |
| 3sa3 | 23X | Protease | / | 0.883 | |
| 3sa5 | A69 | Protease | / | 0.883 | |
| 1z1r | HBH | Gag-Pol polyprotein | 3.4.23.16 | 0.880 | |
| 3nu3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.877 | |
| 3sac | AF8 | Protease | / | 0.877 | |
| 3nuo | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.876 | |
| 3sa7 | 55A | Protease | / | 0.875 | |
| 3nu5 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.872 | |
| 3ttp | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.871 | |
| 4rvj | 478 | Protease | / | 0.862 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.857 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.853 | |
| 4j5j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.849 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.847 | |
| 3s43 | 478 | Protease | / | 0.846 | |
| 3ggu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.844 | |
| 2hs2 | 017 | Protease | / | 0.838 | |
| 2f8g | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.835 | |
| 2fdd | 385 | Pol protein | / | 0.835 | |
| 3sa6 | F71 | Protease | / | 0.831 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.827 | |
| 4hla | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.824 | |
| 1d4l | PI9 | Gag-Pol polyprotein | 3.4.23.16 | 0.815 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.807 | |
| 2psv | MUV | Protease | / | 0.806 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.801 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.796 | |
| 1z1h | HBB | Gag-Pol polyprotein | 3.4.23.16 | 0.791 | |
| 3ekp | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.790 | |
| 3el9 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.781 | |
| 3em4 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.777 | |
| 3sm2 | 478 | Putative gag-pro-pol polyprotein | / | 0.777 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.772 | |
| 1npa | 3NH | Gag-Pol polyprotein | 3.4.23.16 | 0.770 | |
| 1npw | LGZ | Gag-Pol polyprotein | 3.4.23.16 | 0.770 | |
| 2pym | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.750 | |
| 1fej | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.746 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.743 | |
| 1bdr | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.742 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.735 | |
| 2nmy | ROC | Protease | / | 0.732 | |
| 3el1 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.730 | |
| 1mrx | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.729 | |
| 1pro | A88 | Gag-Pol polyprotein | / | 0.728 | |
| 2pk6 | O33 | V-1 protease | / | 0.720 | |
| 2hc0 | AB2 | Protease | / | 0.719 | |
| 1m0b | 0ZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.718 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.718 | |
| 3el0 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.718 | |
| 2q54 | MU1 | Protease | / | 0.717 | |
| 2qi1 | MZ4 | Gag-Pol polyprotein | / | 0.717 | |
| 1d4i | BEG | Gag-Pol polyprotein | 3.4.23.16 | 0.715 | |
| 2q63 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.715 | |
| 3dcr | KVS | Protease | / | 0.715 | |
| 2wkz | 5AH | Gag-Pol polyprotein | / | 0.713 | |
| 3so9 | 017 | Pol protein | / | 0.713 | |
| 3dck | KVI | Protease | / | 0.710 | |
| 3kdb | 006 | Gag-Pol polyprotein | 3.4.23.16 | 0.710 | |
| 2aqu | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.706 | |
| 1b6m | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.705 | |
| 2p3c | 3TL | Protease | / | 0.704 | |
| 3el4 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.704 | |
| 1b6l | PI4 | Gag-Pol polyprotein | 3.4.23.16 | 0.703 | |
| 1hpx | KNI | Gag-Pol polyprotein | / | 0.703 | |
| 1w5x | BE5 | Gag-Pol polyprotein | 3.4.23.16 | 0.700 | |
| 3tl9 | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.700 | |
| 2r38 | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.699 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.698 | |
| 3bxr | DRR | Gag-Pol polyprotein | 3.4.23.16 | 0.697 | |
| 1sdt | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.695 | |
| 3gga | GGW | Gag-Pol polyprotein | / | 0.695 | |
| 1sdu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.694 | |
| 3ndx | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.694 | |
| 1hxb | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.693 | |
| 1k2c | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.693 | |
| 2cej | 1AH | Pol protein | / | 0.693 | |
| 2pyn | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.693 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.690 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.689 | |
| 4k4p | 3TL | Gag-Pol polyprotein | / | 0.688 | |
| 1hih | C20 | Gag-Pol polyprotein | / | 0.687 | |
| 2f3k | RO1 | Protease | / | 0.687 | |
| 1mer | DMQ | Gag-Pol polyprotein | 3.4.23.16 | 0.686 | |
| 2avm | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.686 | |
| 2qak | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.686 | |
| 1daz | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.684 | |
| 1hpv | 478 | Gag-Pol polyprotein | / | 0.684 | |
| 1hxw | RIT | Gag-Pol polyprotein | / | 0.684 | |
| 2nnp | ROC | Protease | / | 0.684 | |
| 3hzc | 2NC | Protease | / | 0.684 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.683 | |
| 2pwr | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.683 | |
| 3fx5 | KNI | Gag-Pol polyprotein | 3.4.23.16 | 0.683 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.683 | |
| 1fg6 | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.682 | |
| 2aoe | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.682 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.682 | |
| 3cyx | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.682 | |
| 9hvp | 0E9 | Gag-Pol polyprotein | / | 0.680 | |
| 1yt9 | OIS | Gag-Pol polyprotein | / | 0.679 | |
| 3ufn | ROC | Gag-Pol polyprotein | / | 0.679 | |
| 1ffi | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.677 | |
| 1hvk | A79 | Gag-Pol polyprotein | / | 0.677 | |
| 1ec1 | BEE | Gag-Pol polyprotein | 3.4.23.16 | 0.676 | |
| 1g2k | NM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.676 | |
| 2pk5 | 075 | Protease | / | 0.675 | |
| 3nyg | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.675 | |
| 1ajv | NMB | Gag-Pol polyprotein | 3.4.23.16 | 0.673 | |
| 2bpy | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.671 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.671 | |
| 1sdv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.670 | |
| 1siv | PSI | Gag-Pol polyprotein | / | 0.669 | |
| 2cen | 4AH | Protease | / | 0.669 | |
| 3ekx | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.668 | |
| 1fff | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.667 | |
| 1a94 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.666 | |
| 2a1e | IPF | Gag-Pol polyprotein | 3.4.23.16 | 0.665 | |
| 1bv7 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.664 | |
| 2p3a | 3TL | Pol protein | / | 0.664 | |
| 2fle | AI | Protease | / | 0.663 | |
| 2uy0 | HV1 | Gag-Pol polyprotein | 3.4.23.16 | 0.663 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.661 | |
| 2p3d | 3TL | Protease | / | 0.661 | |
| 3nxe | 2NC | Protease | / | 0.661 | |
| 3slz | 3TL | Putative gag-pro-pol polyprotein | / | 0.661 | |
| 1b6k | PI5 | Gag-Pol polyprotein | 3.4.23.16 | 0.660 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.660 | |
| 2pqz | G0G | Gag-Pol polyprotein | 3.4.23.16 | 0.660 | |
| 1hvj | A78 | Gag-Pol polyprotein | / | 0.659 | |
| 2bqv | A1A | Protease | / | 0.659 | |
| 1w5v | BE3 | Gag-Pol polyprotein | 3.4.23.16 | 0.658 | |
| 2wl0 | 5AH | Gag-Pol polyprotein | / | 0.658 | |
| 3k4v | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.658 | |
| 3s56 | ROC | Protease | / | 0.658 | |
| 1sh9 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.657 | |
| 2cem | 2AH | Pol protein | / | 0.655 | |
| 2q55 | MU0 | Protease | / | 0.655 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.655 | |
| 1b6p | PI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.653 | |
| 1hvs | A77 | Gag-Pol polyprotein | / | 0.652 | |
| 3a2o | KNJ | Gag-Pol polyprotein | 3.4.23.16 | 0.650 |