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 |
|---|---|---|---|
| 3qtv | 06P | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 1.000 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.834 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.823 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.758 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.753 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.691 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.684 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.675 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.668 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.668 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.651 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.650 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.644 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.642 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.642 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.642 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.642 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.638 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.637 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.635 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.635 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.630 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.621 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.619 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.616 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.615 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.612 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.611 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.609 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.608 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.608 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.602 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.597 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.596 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.593 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.593 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.593 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.591 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.588 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.588 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.588 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.587 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.587 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.587 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.586 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.585 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.583 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.582 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.581 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.579 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.576 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.574 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.574 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.573 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.572 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.572 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.568 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.568 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.568 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.566 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.565 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.563 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.562 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.561 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.561 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.561 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.560 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.559 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.558 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.557 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.550 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.549 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.548 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.545 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.545 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.544 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.541 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.541 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.541 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.540 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.537 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.534 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.533 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.525 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.524 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.520 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.519 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.519 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.518 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.515 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.512 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.511 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.509 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.500 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.492 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.484 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.482 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.481 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.479 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.478 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.478 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.472 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.472 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.470 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.468 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.467 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.464 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 4b0c | C9H | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | 4.2.1.59 | 0.462 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 1fml | RTL | Retinol dehydratase | / | 0.460 | |
| 3wb2 | YGP | Uncharacterized protein MJ0488 | / | 0.460 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 4jsh | Q15 | Nitric oxide synthase, brain | 1.14.13.39 | 0.456 | |
| 5doz | NDP | JamJ | / | 0.456 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.455 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.455 | |
| 3zc5 | W9Z | Hepatocyte growth factor receptor | 2.7.10.1 | 0.455 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.454 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.454 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.454 | |
| 3eku | CY9 | Actin-5C | / | 0.454 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.454 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.454 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.453 | |
| 3eah | 327 | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.453 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.453 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 1qvu | PRL | HTH-type transcriptional regulator QacR | / | 0.451 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3eks | CY9 | Actin-5C | / | 0.451 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.451 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.451 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.451 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.450 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.449 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.449 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.449 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.449 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.449 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 2o12 | FMN | Chorismate synthase | / | 0.448 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.447 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.446 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.446 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.445 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.444 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.444 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.444 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.444 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.443 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.443 | |
| 2v5u | FMN | Flavodoxin | / | 0.443 | |
| 3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.443 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.443 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.443 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.442 | |
| 1rc1 | KT3 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.442 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.442 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.442 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.441 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.440 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.440 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.440 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.440 |