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 Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4bao | MVF | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4bao | MVF | Prothrombin | 3.4.21.5 | 1.000 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.748 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.740 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.735 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.717 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.712 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.708 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.701 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.695 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.679 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.677 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.672 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.667 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.661 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.660 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.657 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.655 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.655 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.651 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.650 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.648 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.647 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.644 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.641 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.638 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.631 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.627 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.621 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.621 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.621 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.618 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.613 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.610 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.610 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.608 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.605 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.603 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.598 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.597 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.596 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.595 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.590 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.590 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.586 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.583 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.582 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.580 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.579 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.579 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.579 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.579 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.579 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.575 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.573 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.573 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.572 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.571 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.568 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.566 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.563 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.562 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.561 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.560 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.558 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.557 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.556 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.555 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.555 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.554 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.554 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.553 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.549 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.547 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.547 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.546 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.545 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.544 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.544 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.543 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.543 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.536 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.534 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.532 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.529 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.527 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.518 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.514 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.506 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.497 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.489 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.474 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.470 | |
| 3eks | CY9 | Actin-5C | / | 0.468 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.466 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.465 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.463 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.462 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.461 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.456 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.452 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.448 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.447 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.445 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.445 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.443 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.443 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.441 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.441 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.440 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.440 |