sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4bao | MVF | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | 0.709 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.708 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.700 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.695 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.682 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.679 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.672 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.658 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.657 | |
| 2zfr | 46U | 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 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.654 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.650 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.647 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.641 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.638 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.633 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.628 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.621 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.621 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.620 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.618 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.614 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.612 | |
| 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 | 0.604 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.603 | |
| 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 | 0.592 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.591 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.585 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.579 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.578 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.577 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.576 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.575 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.574 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.574 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.574 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.574 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.573 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.571 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.571 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.569 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.568 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.568 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.565 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.565 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.565 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.562 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.559 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.557 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.555 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.555 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.553 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.553 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.552 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.547 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.547 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.544 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.538 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.538 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.534 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.528 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.527 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.525 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.525 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.523 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.515 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.514 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.510 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.497 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.470 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.467 | |
| 3eks | CY9 | Actin-5C | / | 0.467 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.460 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.456 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.455 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.453 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.450 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.450 | |
| 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 | 0.447 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.445 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.445 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.442 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.440 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.440 |