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 |
|---|---|---|---|
| 2yj5 | A99 | Copper-transporting ATPase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2yj5 | A99 | Copper-transporting ATPase | / | 1.000 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.483 | |
| 2f3k | RO1 | Protease | / | 0.479 | |
| 3u4l | ATP | Actin, cytoplasmic 1 | / | 0.479 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.476 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.474 | |
| 2uyq | SAM | Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640 | 2.1.1 | 0.473 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.473 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.473 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.469 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.469 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.464 | |
| 3a4o | STU | Tyrosine-protein kinase Lyn | 2.7.10.2 | 0.464 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.463 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.463 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.462 | |
| 2fdd | 385 | Pol protein | / | 0.462 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.462 | |
| 3qp0 | NI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.461 | |
| 3dxm | N24 | Actin-related protein 3 | / | 0.460 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.460 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.459 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.458 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.458 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.458 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.457 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.457 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.457 | |
| 3f47 | I2C | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.457 | |
| 3jvw | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1hpo | UNI | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 2qhc | AB1 | Protease | / | 0.456 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.456 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 4heg | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.455 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.454 | |
| 2bpz | 3IN | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2zb0 | GK3 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3qrm | NK7 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 4j98 | ACP | Fibroblast growth factor receptor 2 | / | 0.454 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 2gcd | STU | Serine/threonine-protein kinase TAO2 | 2.7.11.1 | 0.453 | |
| 2pyn | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.453 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.453 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.453 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3s2p | PMU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.453 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.452 | |
| 1d4y | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2q63 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.452 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.452 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.451 | |
| 3rv8 | RVC | Salicylate synthase | / | 0.451 | |
| 4rcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.451 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.450 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.450 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.450 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.449 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.449 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 2c6k | DT2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2nu9 | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.449 | |
| 2qd8 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.449 | |
| 3gfe | P37 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 3r7y | Z04 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3ufn | ROC | Gag-Pol polyprotein | / | 0.449 | |
| 5aga | ANP | DNA polymerase theta | / | 0.449 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1g2k | NM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1q1w | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.448 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.448 | |
| 2ahc | VNL | Chorismate pyruvate-lyase | / | 0.448 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.448 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2r3t | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3chw | ATP | Major actin | / | 0.448 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.448 | |
| 4e6q | 0NV | Tyrosine-protein kinase JAK2 | / | 0.448 | |
| 4j5j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4l44 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.448 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.448 | |
| 1b7t | ADP | Myosin heavy chain, striated muscle | / | 0.447 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.447 | |
| 2brn | DF1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.447 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.447 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4yd7 | F5N | Endothiapepsin | 3.4.23.22 | 0.447 | |
| 1idb | 0DO | Gag-Pol polyprotein | / | 0.446 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2nnk | ROC | Protease | / | 0.446 | |
| 2r4f | RIE | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.446 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3oxc | ROC | Protease | / | 0.446 | |
| 3oy4 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.446 | |
| 1dq8 | COA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.445 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.445 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.445 | |
| 3t6i | NC9 | Endothiapepsin | 3.4.23.22 | 0.445 | |
| 3upj | U03 | Gag-Pol polyprotein | / | 0.445 | |
| 3vf5 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.445 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.444 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2b8t | THM | Thymidine kinase | / | 0.444 | |
| 2qci | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.444 | |
| 3wze | BAX | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.444 | |
| 4hxy | NDP | Plm1 | / | 0.444 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.444 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.444 | |
| 4ej4 | EJ4 | Delta-type opioid receptor | / | 0.444 | |
| 1g35 | AHF | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ida | 0PO | Gag-Pol polyprotein | 3.4.23.47 | 0.443 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.443 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.443 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.443 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.443 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.443 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.443 | |
| 3t54 | ATP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.443 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.443 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1q8w | M77 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2a1e | IPF | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2f80 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2fxd | DR7 | Pol polyprotein | / | 0.442 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.442 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.442 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.442 | |
| 3pm4 | F5N | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 3s43 | 478 | Protease | / | 0.442 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.442 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2hs2 | 017 | Protease | / | 0.441 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2tmd | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.441 | |
| 2uxz | HI1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2uzo | C62 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3au8 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.441 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3qn8 | NI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.441 | |
| 3sls | 77D | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.441 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.441 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.441 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.441 | |
| 4b1u | LAB | Actin, alpha skeletal muscle | / | 0.441 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.441 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1hpx | KNI | Gag-Pol polyprotein | / | 0.440 | |
| 1k08 | BZD | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.440 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.440 | |
| 2bts | U32 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2uzn | C96 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.440 | |
| 3nu9 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3o3p | GDD | Glycosyl transferase, family 2 | / | 0.440 | |
| 3q5l | KX2 | Heat shock protein 83-1 | / | 0.440 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4m63 | ATP | Actin-5C | / | 0.440 |