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 |
|---|---|---|---|
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 1.000 | |
| 3nhx | ASD | Steroid Delta-isomerase | 5.3.3.1 | 0.582 | |
| 1qjg | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.522 | |
| 3nuv | ASD | Steroid Delta-isomerase | 5.3.3.1 | 0.515 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.484 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.483 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.482 | |
| 3nbr | ASD | Steroid Delta-isomerase | 5.3.3.1 | 0.478 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.478 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.475 | |
| 1osv | CHC | Bile acid receptor | / | 0.472 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.471 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.469 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.468 | |
| 3up3 | XCA | aceDAF-12 | / | 0.466 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.465 | |
| 3tij | URI | Nucleoside permease | / | 0.465 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4few | PP2 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.463 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.462 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2xvv | 9DN | Serum albumin | / | 0.459 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.459 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.458 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.457 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.457 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 4pb2 | 5UD | Nucleoside permease | / | 0.457 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2bxm | IMN | Serum albumin | / | 0.456 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1t02 | LVA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.455 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.453 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.453 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.453 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.452 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.452 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.452 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.452 | |
| 1efa | NPF | Lactose operon repressor | / | 0.451 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 2bxq | IMN | Serum albumin | / | 0.450 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3gxo | MQA | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.450 | |
| 3p9t | TCL | Repressor | / | 0.450 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.449 | |
| 2br1 | PFP | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.449 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.449 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 3hfb | ML4 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.448 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.448 | |
| 3zr7 | OR8 | Progesterone receptor | / | 0.448 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.447 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4j7x | SAS | Sepiapterin reductase | 1.1.1.153 | 0.447 | |
| 4pda | CTN | Nucleoside permease | / | 0.447 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.446 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.446 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.445 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.445 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.445 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.445 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2wqp | WQP | Polysialic acid capsule biosynthesis protein SiaC | / | 0.444 | |
| 3b9l | AZZ | Serum albumin | / | 0.444 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.444 | |
| 4bhw | 01K | Histone acetyltransferase p300 | / | 0.444 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3qge | 26F | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.442 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.442 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3uhm | RFN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.442 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 5dhh | DGW | Nociceptin receptor | / | 0.442 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.441 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.440 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.440 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.440 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.440 |