sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 1.000 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.714 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.650 | |
| 2agv | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.617 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.610 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.604 | |
| 3nal | DBK | Calcium-transporting ATPase | / | 0.583 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.509 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.498 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.495 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.489 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.487 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.482 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.479 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.478 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.475 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.474 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.473 | |
| 3aba | FLI | Cytochrome P450 | / | 0.471 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.471 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 4l8u | 9AZ | Serum albumin | / | 0.468 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.467 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.467 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.467 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3zkp | ERB | Erythromycin C-12 hydroxylase | 1.14.13.154 | 0.465 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.464 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.463 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.462 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.461 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.461 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.461 | |
| 3lu8 | IQX | Serum albumin | / | 0.461 | |
| 4l9k | EHF | Serum albumin | / | 0.461 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1ppj | ANY | Cytochrome b | / | 0.459 | |
| 4phl | PIL | Phosphodiesterase | / | 0.459 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.458 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.458 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.458 | |
| 4gue | QCT | Ribosomal protein S6 kinase alpha-3 | 2.7.11.1 | 0.458 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.458 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.458 | |
| 2gd0 | MRS | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.457 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.457 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.457 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.457 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.456 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.456 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.456 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 1ysx | 4EB | Serum albumin | / | 0.455 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.455 | |
| 2gci | MRR | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.455 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3gc8 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.455 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.454 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.453 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.452 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.452 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.452 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.451 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.451 | |
| 2imk | GTX | AGAP009194-PA | / | 0.451 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.451 | |
| 4el9 | AFE | Ribosomal protein S6 kinase alpha-3 | 2.7.11.1 | 0.451 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.451 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.451 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.449 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.448 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.448 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.447 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.447 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.447 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.446 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.446 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.446 | |
| 4l9q | 9TP | Serum albumin | / | 0.446 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.445 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.445 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.445 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.444 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.444 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.444 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 3tgu | WF3 | Cytochrome b | / | 0.444 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.444 | |
| 4jvm | XDI | Estrogen sulfotransferase | 2.8.2.4 | 0.444 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.443 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.443 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 1ek2 | CDU | Bifunctional epoxide hydrolase 2 | / | 0.442 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.440 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.440 |