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 |
|---|---|---|---|
| 2b96 | ANN | Phospholipase A2 | 3.1.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2b96 | ANN | Phospholipase A2 | 3.1.1.4 | 1.000 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.560 | |
| 3nju | ANN | Acidic phospholipase A2 3 | 3.1.1.4 | 0.557 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.535 | |
| 1y6o | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.533 | |
| 1fdk | GLE | Phospholipase A2 | 3.1.1.4 | 0.522 | |
| 1db4 | 8IN | Phospholipase A2, membrane associated | / | 0.511 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.510 | |
| 1o2e | ANN | Phospholipase A2 | 3.1.1.4 | 0.508 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.487 | |
| 1fxf | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.486 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.485 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.484 | |
| 1db5 | 6IN | Phospholipase A2, membrane associated | / | 0.481 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.480 | |
| 4n1g | CEI | Obelin | / | 0.479 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.478 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.476 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.476 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.475 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.474 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.474 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.472 | |
| 4qg1 | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.470 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.469 | |
| 1a8t | 061 | Metallo-beta-lactamase type 2 | / | 0.468 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.468 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.468 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 1u1j | C2F | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 | 2.1.1.14 | 0.466 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.466 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 4olf | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.466 | |
| 2fxf | ACO | Diamine acetyltransferase 1 | / | 0.464 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 4fj0 | HHF | 17beta-hydroxysteroid dehydrogenase | / | 0.464 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.463 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.462 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3qgi | 33F | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.460 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.459 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.458 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.458 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.458 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.458 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.457 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.457 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.457 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 5epe | SAH | Uncharacterized protein | / | 0.457 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.456 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.456 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.456 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.455 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.455 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.455 | |
| 2b99 | RDL | Riboflavin synthase | 2.5.1.9 | 0.454 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.454 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 3tfp | 03L | Dehydrosqualene synthase | / | 0.454 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.453 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.452 | |
| 1muu | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.452 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.452 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.452 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.452 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.452 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.452 | |
| 4to1 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.452 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.452 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.452 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.451 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.451 | |
| 4dyb | 0MH | Nucleoprotein | / | 0.451 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.451 | |
| 1c7o | PPG | Hemolysin | / | 0.450 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.450 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.450 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.450 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.450 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.450 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.449 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.449 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.449 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.448 | |
| 3qwh | KMP | 17beta-hydroxysteroid dehydrogenase | / | 0.448 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.448 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.448 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.447 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.447 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.446 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.446 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.446 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.446 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.446 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.446 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.446 | |
| 4fiz | CUE | 17beta-hydroxysteroid dehydrogenase | / | 0.446 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.446 | |
| 1m8j | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.445 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2cje | DUN | DUTPase | / | 0.445 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.445 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.445 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.444 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 4amj | CVD | Beta-1 adrenergic receptor | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.444 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.444 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.444 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.443 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2w02 | ATP | AcsD | / | 0.443 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.443 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.443 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.443 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2c6c | 24I | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.442 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.442 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.441 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.441 | |
| 4kxj | P34 | Nucleoprotein | / | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.440 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.440 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.440 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.440 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.440 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.440 |