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 |
|---|---|---|---|
| 3bi4 | 298 | Polyamine oxidase FMS1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3bi4 | 298 | Polyamine oxidase FMS1 | / | 1.000 | |
| 3bnm | SPJ | Polyamine oxidase FMS1 | / | 0.589 | |
| 3cnp | SP7 | Polyamine oxidase FMS1 | / | 0.584 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.493 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.491 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.489 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.486 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.484 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.481 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.481 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.480 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.476 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.476 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.475 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.475 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.471 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.471 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.470 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.468 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.467 | |
| 5dp2 | NAP | CurF | / | 0.465 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.463 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.463 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.462 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.462 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.462 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.462 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.462 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.462 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.462 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.461 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.461 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.460 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.460 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.459 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.458 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.457 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.457 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.456 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.456 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.456 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.456 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 2eka | SAH | Diphthine synthase | / | 0.455 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.455 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.455 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.455 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.454 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.454 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.454 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.454 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.454 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.454 | |
| 3e4a | QIX | Insulin-degrading enzyme | 3.4.24.56 | 0.454 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.454 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.454 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.454 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.454 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.454 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.454 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.453 | |
| 1lbb | KAI | Glutamate receptor 2 | / | 0.453 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.453 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.453 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.453 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.453 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.452 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.452 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.452 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.452 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.451 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.451 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.450 | |
| 4ck2 | NVU | Integrase | / | 0.450 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.449 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 5ccy | TMP | Polymerase acidic protein | / | 0.449 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.448 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.448 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2o8j | SAH | Histone-lysine N-methyltransferase EHMT2 | / | 0.448 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.448 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.448 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.448 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.447 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.447 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.447 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.447 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.446 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.446 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.446 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.446 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.446 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.446 | |
| 3e78 | TPP | High affinity transport system protein p37 | / | 0.446 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.446 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.446 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.446 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.445 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.445 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.445 | |
| 2nr4 | FMN | Conserved protein | / | 0.445 | |
| 3hr4 | FMN | Nitric oxide synthase, inducible | 1.14.13.39 | 0.445 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.445 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.445 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.445 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.444 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.444 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.444 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.444 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.444 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.443 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.443 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.443 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.443 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.442 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.442 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.442 | |
| 3esz | FMN | Flavodoxin | / | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.441 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.441 | |
| 2v19 | FMN | Dodecin | / | 0.441 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.441 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.441 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.441 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.441 | |
| 4ekg | 0QJ | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.441 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.440 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.440 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.440 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.440 | |
| 4nv1 | TYD | Formyl transferase | / | 0.440 | |
| 5egh | PC | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | / | 0.440 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.440 |