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 |
|---|---|---|---|
| 1sqb | AZO | Cytochrome b |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1sqb | AZO | Cytochrome b | / | 1.000 | |
| 3l71 | AZO | Cytochrome b | / | 0.608 | |
| 3l70 | JZV | Cytochrome b | / | 0.595 | |
| 1sqp | MYX | Cytochrome b | / | 0.556 | |
| 1sqq | OST | Cytochrome b | / | 0.523 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.488 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.473 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.466 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.466 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.464 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.463 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.461 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.460 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3cr7 | PPS | Adenylyl-sulfate kinase | 2.7.1.25 | 0.459 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.459 | |
| 1ohk | COP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.458 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.458 | |
| 1ddt | APU | Diphtheria toxin | / | 0.457 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.457 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.456 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.454 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.454 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.454 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.453 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.453 | |
| 4klr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 1fcx | 184 | Retinoic acid receptor gamma | / | 0.452 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.452 | |
| 4boe | CLR | Japanin | / | 0.452 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.452 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.451 | |
| 2gpv | OHT | Estrogen-related receptor gamma | / | 0.451 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.451 | |
| 4iae | 1DX | Alr2278 protein | / | 0.451 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.449 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.449 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.449 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.449 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.449 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.449 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.448 | |
| 4iah | 1DX | Alr2278 protein | / | 0.448 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.447 | |
| 1t47 | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.446 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 1ezv | SMA | Cytochrome b | / | 0.445 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 3hyw | DCQ | Sulfide-quinone reductase | / | 0.445 | |
| 4hdr | DMD | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | / | 0.445 | |
| 4hdr | DMD | ArsB | / | 0.445 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.445 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 2pnu | ENM | Androgen receptor | / | 0.444 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.444 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.444 | |
| 4a9i | P9I | Bromodomain-containing protein 2 | / | 0.444 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.444 | |
| 4mm9 | FVX | Na(+):neurotransmitter symporter (Snf family) | / | 0.444 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.444 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.443 | |
| 2yiu | SMA | Cytochrome b | / | 0.443 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.443 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.443 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.442 | |
| 1uom | PTI | Estrogen receptor | / | 0.442 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2x21 | PID | Peridinin-chlorophyll a-binding protein 1, chloroplastic | / | 0.442 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.442 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.442 | |
| 5d7p | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.442 | |
| 1ppj | SMA | Cytochrome b | / | 0.441 | |
| 1pt8 | ACO | Formyl-CoA:oxalate CoA-transferase | / | 0.441 | |
| 1yin | CM3 | Estrogen receptor | / | 0.441 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.441 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.441 | |
| 5d7q | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.441 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.440 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3iis | PID | Peridinin-chlorophyll a-binding protein 1, chloroplastic | / | 0.440 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.440 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 |