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 |
|---|---|---|---|
| 1iqe | XMB | Coagulation factor X | 3.4.21.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1iqe | XMB | Coagulation factor X | 3.4.21.6 | 1.000 | |
| 1iqg | XME | Coagulation factor X | 3.4.21.6 | 0.576 | |
| 2cji | GSK | Coagulation factor X | 3.4.21.6 | 0.543 | |
| 2g00 | 4QC | Coagulation factor X | 3.4.21.6 | 0.538 | |
| 1nfy | RTR | Coagulation factor X | 3.4.21.6 | 0.520 | |
| 1zsk | 421 | Coagulation factor XI | 3.4.21.27 | 0.502 | |
| 4btu | 6XS | Coagulation factor X | 3.4.21.6 | 0.500 | |
| 1sqt | UI3 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.490 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.488 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.483 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.482 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.482 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.480 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.479 | |
| 1vja | 7IN | Urokinase-type plasminogen activator | 3.4.21.73 | 0.476 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.475 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.474 | |
| 1lqd | CMI | Coagulation factor X | 3.4.21.6 | 0.473 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.473 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.473 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.471 | |
| 3v0x | ANH | Cationic trypsin | 3.4.21.4 | 0.471 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.470 | |
| 2y5g | FJD | Coagulation factor X | 3.4.21.6 | 0.470 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.470 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.470 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.469 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.468 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.468 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.467 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.467 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.467 | |
| 3dxm | N24 | Actin-related protein 3 | / | 0.466 | |
| 4bti | 7R9 | Coagulation factor X | 3.4.21.6 | 0.466 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.465 | |
| 1iqh | XMF | Coagulation factor X | 3.4.21.6 | 0.465 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.465 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.464 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.464 | |
| 2viv | VG2 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.464 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.464 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.464 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.462 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.462 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.462 | |
| 1owe | 675 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.461 | |
| 3plp | BBA | Cationic trypsin | 3.4.21.4 | 0.461 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.461 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.460 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.460 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.460 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.460 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.459 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.459 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.459 | |
| 4l4x | NDP | AmphI | / | 0.459 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.458 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.458 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.458 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.457 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.457 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 3u9e | COA | Lmo1369 protein | / | 0.456 | |
| 3v2u | ATP | Protein GAL3 | / | 0.456 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.456 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.456 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.455 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.455 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.455 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.455 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.455 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.455 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.455 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.454 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.453 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.453 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.453 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.453 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.453 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.452 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.452 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.452 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.452 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.452 | |
| 2emu | SAH | Diphthine synthase | / | 0.451 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.451 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.450 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.450 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.450 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.450 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.450 | |
| 1m75 | CAA | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3eks | CY9 | Actin-5C | / | 0.449 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.449 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.449 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.449 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.449 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.448 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.448 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.448 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.447 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.447 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.447 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 5a3b | APR | SIR2 family protein | / | 0.447 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.446 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.446 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.445 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.445 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.445 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.445 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.445 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.444 | |
| 2eka | SAH | Diphthine synthase | / | 0.444 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.444 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.444 | |
| 5jjs | SAH | Genome polyprotein | / | 0.444 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.443 | |
| 1mma | ADP | Myosin-2 heavy chain | / | 0.443 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.443 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.443 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.443 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.442 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1gmc | PRO_GLY_ALA_TYR | Chymotrypsinogen A | 3.4.21.1 | 0.442 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.442 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.442 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.442 | |
| 2e16 | SAH | Diphthine synthase | / | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.442 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.442 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.442 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.442 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.442 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.442 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.441 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.441 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.441 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.440 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.440 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.440 | |
| 4rww | 2BA | Lmo2692 protein | / | 0.440 |