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 |
|---|---|---|---|
| 2zf0 | 51U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.779 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.778 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.774 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.755 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.748 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.742 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.739 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.727 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.722 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.706 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.704 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.694 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.690 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.688 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.679 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.675 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.675 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.673 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.672 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.668 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.660 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.660 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.657 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.652 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.650 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.649 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.648 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.646 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.643 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.640 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.639 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.637 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.631 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.629 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.629 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.628 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.627 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.627 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.625 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.624 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.623 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.622 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.621 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.618 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.616 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.614 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.613 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.610 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.609 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.607 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.606 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.605 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.603 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.600 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.600 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.595 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.594 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.593 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.590 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.590 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.588 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.581 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.577 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.576 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.576 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.575 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.573 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.570 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.569 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.566 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.565 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.561 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.561 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.555 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.545 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.542 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.537 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.534 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.533 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.527 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.527 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.527 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.523 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.522 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.516 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.515 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.513 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.508 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.506 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.501 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.500 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.498 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.492 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.487 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.484 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.482 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.478 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.476 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.474 | |
| 2ele | SAH | Diphthine synthase | / | 0.472 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.472 | |
| 2p6d | SAH | Diphthine synthase | / | 0.471 | |
| 2ejz | SAH | Diphthine synthase | / | 0.470 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.470 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.469 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.467 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.466 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 2ejk | SAH | Diphthine synthase | / | 0.465 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.465 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.464 | |
| 2ehl | SAH | Diphthine synthase | / | 0.464 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.464 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 1fml | RTL | Retinol dehydratase | / | 0.460 | |
| 2emu | SAH | Diphthine synthase | / | 0.459 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.458 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.455 | |
| 2e7r | SAH | Diphthine synthase | / | 0.455 | |
| 2eka | SAH | Diphthine synthase | / | 0.455 | |
| 2e8r | SAH | Diphthine synthase | / | 0.453 | |
| 2egb | SAH | Diphthine synthase | / | 0.453 | |
| 2owk | SAH | Diphthine synthase | / | 0.453 | |
| 2e16 | SAH | Diphthine synthase | / | 0.452 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.452 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.452 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.451 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 2emr | SAH | Diphthine synthase | / | 0.450 | |
| 3eku | CY9 | Actin-5C | / | 0.449 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.449 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.448 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.447 | |
| 2pck | SAH | Diphthine synthase | / | 0.447 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.446 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.446 | |
| 2dxx | SAH | Diphthine synthase | / | 0.446 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.446 | |
| 2pci | SAH | Diphthine synthase | / | 0.446 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 2pcg | SAH | Diphthine synthase | / | 0.445 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 1vce | SAH | Diphthine synthase | / | 0.444 | |
| 2dek | SAH | Diphthine synthase | / | 0.444 | |
| 2pch | SAH | Diphthine synthase | / | 0.444 | |
| 3eks | CY9 | Actin-5C | / | 0.444 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.443 | |
| 2e08 | SAH | Diphthine synthase | / | 0.443 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.443 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.442 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 2owg | SAH | Diphthine synthase | / | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.442 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.442 | |
| 4yfy | 0FX | VioF | / | 0.442 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.441 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2huv | SAH | Diphthine synthase | / | 0.440 |