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 |
|---|---|---|---|
| 2ony | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ony | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 1.000 | |
| 2onz | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.770 | |
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.761 | |
| 2obf | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.651 | |
| 2g8n | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.603 | |
| 2g72 | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.562 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.508 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.493 | |
| 1re0 | AFB | ADP-ribosylation factor 1 | / | 0.491 | |
| 1re0 | AFB | ARF guanine-nucleotide exchange factor 1 | / | 0.491 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.484 | |
| 3arv | SAU | Chitinase A | / | 0.482 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.480 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.478 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.477 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.475 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.475 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.475 | |
| 1lcw | SHM | Streptavidin | / | 0.474 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.474 | |
| 3mp5 | HMG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.474 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.473 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.472 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.471 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.470 | |
| 2yhu | WHF | Pteridine reductase | / | 0.469 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.468 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.468 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.468 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.467 | |
| 4rsy | B3N | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.466 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.465 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.464 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 4ixc | 1JD | Glucokinase | 2.7.1.2 | 0.464 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.463 | |
| 3lm4 | HPX | Catechol 2,3-dioxygenase | / | 0.463 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.462 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.461 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.461 | |
| 4nqg | CZH | Mitrocomin | / | 0.461 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.461 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.460 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.460 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.459 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.459 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.458 | |
| 2wat | COA | Fatty acid synthase subunit alpha | 2.3.1.86 | 0.458 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.458 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.458 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4mzu | TYD | WxcM-like protein | / | 0.458 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.457 | |
| 3ftx | RE2 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.457 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.457 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.457 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.457 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.456 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.456 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 3chs | 4BU | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.455 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.455 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.454 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.454 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.454 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.453 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.453 | |
| 3w5u | FAD | Ferredoxin | / | 0.453 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.453 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.453 | |
| 4k4e | K4E | Tankyrase-1 | 2.4.2.30 | 0.453 | |
| 4l09 | 1UR | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4n1f | CZH | Obelin | / | 0.453 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.453 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.452 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.452 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2fxf | ACO | Diamine acetyltransferase 1 | / | 0.452 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.452 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.452 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.452 | |
| 3mtw | M3R | Xaa-Pro dipeptidase, putative | / | 0.452 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.452 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.452 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.451 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.451 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.451 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.451 | |
| 4ggz | BTN | Bll1558 protein | / | 0.451 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.450 | |
| 1jf0 | CZH | Obelin | / | 0.449 | |
| 2jdd | ACO | Probable acetyltransferase | / | 0.449 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.449 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.449 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4k4f | K4F | Tankyrase-1 | 2.4.2.30 | 0.449 | |
| 1uhh | CZP | Aequorin-2 | / | 0.448 | |
| 1ye6 | NAP | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.448 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.448 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.448 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.448 | |
| 4a6n | T1C | TetX family tetracycline inactivation enzyme | / | 0.448 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.448 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.447 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.447 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.447 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.446 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.446 | |
| 3ful | 52D | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.446 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.446 | |
| 3tfy | MET_LEU_GLY_PRO | N-alpha-acetyltransferase 50 | 2.3.1 | 0.446 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.446 | |
| 4gd9 | BTN | Streptavidin | / | 0.446 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.446 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2hyy | STI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.445 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.445 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.445 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.445 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.445 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.444 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.444 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.444 | |
| 4g67 | SAH | Uncharacterized ACR, COG1565 superfamily | / | 0.444 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.444 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1wl4 | COA | Acetyl-CoA acetyltransferase, cytosolic | 2.3.1.9 | 0.443 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.443 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.443 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.443 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4ivy | 1GT | Estrogen receptor | / | 0.443 | |
| 1ez0 | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.442 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.442 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.442 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 4x9d | U5P | Uncharacterized protein MJ1435 | / | 0.442 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1sjw | NGV | Nogalonic acid methyl ester cyclase | / | 0.441 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.441 | |
| 2bsw | CAO | Probable acetyltransferase | / | 0.441 | |
| 2dxf | GNP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.441 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.441 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.441 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.441 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3r94 | FLR | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4py6 | R78 | Bromodomain protein, putative | / | 0.441 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.440 | |
| 2qhx | FE1 | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.440 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.440 | |
| 3pg3 | DG7 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.440 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.440 |