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 |
|---|---|---|---|
| 1ghv | 120 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 1.000 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.694 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.689 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.674 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.673 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.671 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.669 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.666 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.663 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.653 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.652 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.648 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.646 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.642 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.641 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.639 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.639 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.638 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.636 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.632 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.631 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.630 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.630 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.628 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.625 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.623 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.618 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.615 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.615 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.614 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.613 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.613 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.612 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.611 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.606 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.601 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.601 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.600 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.599 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.599 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.599 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.598 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.597 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.597 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.597 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.596 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.594 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.594 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.591 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.590 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.589 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.588 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.587 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.587 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.585 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.585 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.583 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.583 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.581 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.581 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.580 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.580 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.579 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.577 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.577 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.577 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.574 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.573 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.573 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.572 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.571 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.570 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.570 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.569 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.566 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.565 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.563 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.562 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.561 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.558 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.556 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.551 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.551 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.551 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.549 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.546 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.546 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.545 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.541 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.540 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.539 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.537 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.530 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.529 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.525 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.521 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.518 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.513 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.506 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.496 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.483 | |
| 2z3l | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.483 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.482 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.481 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.480 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.479 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.475 | |
| 2p2x | SAH | Diphthine synthase | / | 0.464 | |
| 2p5c | SAH | Diphthine synthase | / | 0.464 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.462 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.462 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.459 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.459 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.459 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.457 | |
| 2e7r | SAH | Diphthine synthase | / | 0.453 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.452 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.452 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.451 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.451 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.451 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.449 | |
| 1fml | RTL | Retinol dehydratase | / | 0.448 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.445 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.444 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.444 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2p6k | SAH | Diphthine synthase | / | 0.442 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.441 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.441 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.440 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.440 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.440 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.440 |