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 |
|---|---|---|---|
| 4cgi | NZL | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cgi | NZL | Integrase | / | 1.000 | |
| 3zsv | ZSV | Integrase | / | 0.667 | |
| 4ceb | ZSV | Integrase | / | 0.667 | |
| 4cgd | 8P3 | Integrase | / | 0.618 | |
| 4cec | 2SS | Integrase | / | 0.603 | |
| 4ceq | QCH | Integrase | / | 0.599 | |
| 4cfd | S8Y | Integrase | / | 0.589 | |
| 4cfb | OM3 | Integrase | / | 0.588 | |
| 3zsr | O3N | Integrase | / | 0.586 | |
| 4cez | O3N | Integrase | / | 0.586 | |
| 4ceo | G0T | Integrase | / | 0.583 | |
| 4cgj | NZL | Integrase | / | 0.580 | |
| 4cjf | RVN | Integrase | / | 0.579 | |
| 4cfa | WOP | Integrase | / | 0.575 | |
| 4cf2 | 3GM | Integrase | / | 0.574 | |
| 4cfc | 7NV | Integrase | / | 0.574 | |
| 4ces | NFW | Integrase | / | 0.572 | |
| 4chq | CWU | Integrase | / | 0.572 | |
| 3zt3 | ZT4 | Integrase | / | 0.571 | |
| 4cf8 | V7H | Integrase | / | 0.571 | |
| 3zsw | ZSW | Integrase | / | 0.570 | |
| 4cef | D0T | Integrase | / | 0.569 | |
| 4chy | C5Q | Integrase | / | 0.569 | |
| 4cju | JNS | Integrase | / | 0.569 | |
| 4cj4 | S3G | Integrase | / | 0.567 | |
| 4cie | Y7N | Integrase | / | 0.565 | |
| 4cj3 | E4F | Integrase | / | 0.563 | |
| 4ck1 | OM1 | Integrase | / | 0.562 | |
| 4cea | ZSW | Integrase | / | 0.561 | |
| 4cer | VL4 | Integrase | / | 0.560 | |
| 4cf1 | IY7 | Integrase | / | 0.558 | |
| 4ce9 | O3N | Integrase | / | 0.557 | |
| 4ced | 9NS | Integrase | / | 0.557 | |
| 4cjq | VXO | Integrase | / | 0.557 | |
| 3zsy | OM3 | Integrase | / | 0.556 | |
| 4ck2 | NVU | Integrase | / | 0.555 | |
| 4cgg | K5Q | Integrase | / | 0.551 | |
| 4cig | X0P | Integrase | / | 0.550 | |
| 3zt2 | ZT2 | Integrase | / | 0.547 | |
| 4cif | JDX | Integrase | / | 0.547 | |
| 4cj5 | 4VW | Integrase | / | 0.543 | |
| 4cjk | H39 | Integrase | / | 0.543 | |
| 4cgh | LOZ | Integrase | / | 0.542 | |
| 4cjp | 4D2 | Integrase | / | 0.542 | |
| 4cee | B0T | Integrase | / | 0.540 | |
| 4cje | Q31 | Integrase | / | 0.540 | |
| 4ck3 | K1T | Integrase | / | 0.540 | |
| 3zsx | N44 | Integrase | / | 0.538 | |
| 3zt1 | OM1 | Integrase | / | 0.536 | |
| 3zt0 | ZT0 | Integrase | / | 0.535 | |
| 4cf0 | O5U | Integrase | / | 0.530 | |
| 4cjs | L0Y | Integrase | / | 0.525 | |
| 3zsq | O4N | Integrase | / | 0.516 | |
| 3zsz | OM2 | Integrase | / | 0.512 | |
| 4cjr | FYM | Integrase | / | 0.501 | |
| 3zcm | PX3 | Integrase | / | 0.500 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.480 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.478 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.472 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.471 | |
| 2xvu | 9DN | Serum albumin | / | 0.470 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.470 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.468 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.467 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.466 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 3up0 | D7S | aceDAF-12 | / | 0.464 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.462 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.461 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.461 | |
| 3daf | FEG | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.461 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.460 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.459 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2ohv | NHL | Glutamate racemase | / | 0.459 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.459 | |
| 4bzo | 676 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.459 | |
| 4cgf | UJ6 | Integrase | / | 0.459 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.458 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.457 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.457 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.456 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.456 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.456 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.456 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.455 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.455 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.453 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.453 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.452 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.452 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.452 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.452 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.451 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1y57 | MPZ | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.451 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.451 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4a4z | ANP | Antiviral helicase SKI2 | 3.6.4.13 | 0.451 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.451 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.451 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.450 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.450 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.450 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.449 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.449 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.448 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.448 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.448 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.448 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.448 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.448 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.448 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.447 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.447 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.447 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.447 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.446 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3cy2 | MB9 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.446 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.445 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.445 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.445 | |
| 2cts | COA | Citrate synthase, mitochondrial | 2.3.3.1 | 0.445 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.445 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.445 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.445 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.445 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1gqt | ACP | Ribokinase | / | 0.444 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.444 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.444 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.444 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.444 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5ebu | FMN | Lactate oxidase | / | 0.444 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.443 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.443 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.443 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.443 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.442 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.442 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.442 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.442 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.442 | |
| 1axw | MTX | Thymidylate synthase | / | 0.441 | |
| 1b8u | NAD | Malate dehydrogenase | / | 0.441 | |
| 1fml | RTL | Retinol dehydratase | / | 0.441 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.441 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.441 | |
| 2j4k | U5P | Uridylate kinase | 2.7.4.22 | 0.441 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.441 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3n6u | TSU | HTH-type transcriptional regulator TsaR | / | 0.441 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 5e8y | STU | TGF-beta receptor type-2 | 2.7.11.30 | 0.441 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.440 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.440 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.440 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2e9n | 76A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 2oj9 | BMI | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.440 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.440 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |