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 |
|---|---|---|---|
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.712 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.675 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.644 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.624 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.623 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.592 | |
| 2ejz | SAH | Diphthine synthase | / | 0.498 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.496 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.483 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.472 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.467 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.467 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.466 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.462 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.462 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.461 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.461 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.459 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.458 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.455 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.455 | |
| 4wbd | ADP | Putative cysteine ligase BshC | / | 0.455 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.454 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.454 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.453 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.453 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.453 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.453 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.452 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.452 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4j7g | TRH | PCZA361.3 | / | 0.451 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.449 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.448 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.448 | |
| 3n0b | FAD | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4j7h | TRH | PCZA361.3 | / | 0.447 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.447 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.446 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.445 | |
| 2cns | ACO | Ribosomal-protein-alanine acetyltransferase | / | 0.445 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.444 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.444 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.444 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.444 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.443 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.442 | |
| 2b99 | RDL | Riboflavin synthase | 2.5.1.9 | 0.442 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.442 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1gaw | FAD | Ferredoxin | / | 0.441 | |
| 1isg | AGS | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 | 0.441 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.441 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4krs | 1SX | Tankyrase-1 | 2.4.2.30 | 0.440 |