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 |
|---|---|---|---|
| 2jfz | 003 | Glutamate racemase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2jfz | 003 | Glutamate racemase | / | 1.000 | |
| 4b1f | KRH | Glutamate racemase | / | 0.636 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.506 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.491 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.484 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.480 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.477 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.475 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.474 | |
| 4b8w | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.474 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.473 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.470 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.469 | |
| 2wpx | ACO | Orf14 | / | 0.468 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.465 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.465 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.465 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.463 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.463 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.462 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.462 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.462 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.460 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.460 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3up0 | D7S | aceDAF-12 | / | 0.460 | |
| 4l8u | 9AZ | Serum albumin | / | 0.460 | |
| 4l9q | 9TP | Serum albumin | / | 0.460 | |
| 2c3i | IYZ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.459 | |
| 2hek | GDP | Uncharacterized protein | / | 0.459 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.459 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.458 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.458 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.458 | |
| 4awi | AQ2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.458 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.458 | |
| 1osv | CHC | Bile acid receptor | / | 0.457 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.457 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.457 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.457 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.456 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.456 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.456 | |
| 1ci7 | CB3 | Thymidylate synthase | 2.1.1.45 | 0.455 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.455 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.455 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.455 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.454 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.454 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.454 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.454 | |
| 4o7u | THF | Thymidylate synthase | / | 0.454 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.454 | |
| 1bq1 | CB3 | Thymidylate synthase | / | 0.453 | |
| 1zdw | FLV | Prenyltransferase | / | 0.453 | |
| 3a60 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.453 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.452 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2j4z | 626 | Aurora kinase A | 2.7.11.1 | 0.452 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.452 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.452 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.451 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3pg3 | DG7 | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 3q9z | TXQ | Casein kinase II subunit alpha | 2.7.11.1 | 0.451 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.451 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.451 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.450 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 3ma3 | 01I | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.450 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.449 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.449 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.449 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.449 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.449 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.448 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.448 | |
| 3fko | FKO | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3gdv | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.448 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.448 | |
| 4l9k | EHF | Serum albumin | / | 0.448 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.447 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.447 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.447 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.447 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.446 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4fog | C2F | Thymidylate synthase ThyA | / | 0.446 | |
| 4o4f | ATP | Kinase | / | 0.446 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.445 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.445 | |
| 2w0b | CMW | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.445 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3lu8 | IQX | Serum albumin | / | 0.445 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.445 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3up3 | XCA | aceDAF-12 | / | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.445 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 5doz | NDP | JamJ | / | 0.445 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 1syn | F89 | Thymidylate synthase | / | 0.444 | |
| 2gd2 | CAA | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.444 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3fl4 | FL4 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 3w2c | N15 | Aurora kinase A | 2.7.11.1 | 0.444 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.444 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 5ikq | JMS | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.444 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.443 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.443 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.443 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.443 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.443 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.442 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.442 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2wpw | ACO | Orf14 | / | 0.442 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.442 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.442 | |
| 3zs5 | SB2 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 1hnc | GDN | Glutathione S-transferase Mu 2 | 2.5.1.18 | 0.441 | |
| 1juj | LYA | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.441 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.441 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 3bac | 3B9 | DNA ligase | / | 0.441 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.441 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.441 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 4iqq | D16 | Thymidylate synthase | / | 0.441 | |
| 4lm5 | Q17 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.441 | |
| 1a2n | TET | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.440 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1e94 | ANP | ATP-dependent protease ATPase subunit HslU | / | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.440 | |
| 1zzl | TZY | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.440 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3bhl | THG | Thymidylate synthase | / | 0.440 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.440 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.440 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.440 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4iae | 1DX | Alr2278 protein | / | 0.440 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.440 |