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 |
|---|---|---|---|
| 3m6l | TPP | Transketolase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3m6l | TPP | Transketolase | / | 1.000 | |
| 3m34 | TPP | Transketolase | / | 0.594 | |
| 4c7x | TPP | Transketolase | / | 0.547 | |
| 3m7i | TPP | Transketolase | / | 0.539 | |
| 3upt | TPP | Transketolase | / | 0.518 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.491 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.491 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.488 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.486 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.484 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.480 | |
| 4iah | 1DX | Alr2278 protein | / | 0.480 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.480 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.479 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.478 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.477 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.476 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.476 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.475 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.474 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.474 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.473 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.472 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.472 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.471 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.471 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.470 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.469 | |
| 2w03 | ADN | AcsD | / | 0.468 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.467 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.467 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.466 | |
| 3b82 | NAD | Exotoxin A | 2.4.2.36 | 0.465 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.464 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.464 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.464 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.464 | |
| 3smk | CW7 | 14-3-3 protein sigma | / | 0.463 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.462 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.462 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.461 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.461 | |
| 4std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.461 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.460 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.460 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.460 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.458 | |
| 2k62 | ITL | Fatty acid-binding protein, liver | / | 0.458 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.458 | |
| 4ww4 | ADP | RuvB-like helicase | / | 0.458 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.457 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.457 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.457 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.457 | |
| 1e2n | RCA | Thymidine kinase | / | 0.456 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.456 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.456 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.456 | |
| 2w02 | ATP | AcsD | / | 0.456 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.456 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.456 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.455 | |
| 2gtb | AZP | Orf1ab polyprotein | / | 0.455 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.455 | |
| 3iog | SDF | Metallo-beta-lactamase type 2 | / | 0.455 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.455 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.454 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.454 | |
| 4h7z | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.454 | |
| 1x28 | PGU | Aspartate aminotransferase | 2.6.1.1 | 0.453 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.453 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.453 | |
| 4ivr | N50 | Thymidine kinase | / | 0.453 | |
| 4oma | LCS | Methionine gamma-lyase | / | 0.453 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.453 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.452 | |
| 4r2m | ANP | Universal stress protein F | / | 0.452 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.451 | |
| 1wpg | ADP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.451 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.451 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.451 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.451 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.451 | |
| 5bnw | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.451 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.450 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.450 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.450 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.450 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 1trk | TPP | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.449 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.448 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 3rim | TPP | Transketolase | 2.2.1.1 | 0.448 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.448 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.448 | |
| 4pd6 | URI | Nucleoside permease | / | 0.448 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 2ejz | SAH | Diphthine synthase | / | 0.447 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.447 | |
| 2vku | DBE | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.447 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.447 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.446 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.446 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 2qvd | BER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.446 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 5c80 | URI | Uridine phosphorylase | / | 0.446 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.445 | |
| 2i6a | 5I5 | Adenosine kinase | 2.7.1.20 | 0.445 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2qwq | ADP | Heat shock cognate 71 kDa protein | / | 0.445 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.445 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.445 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.445 | |
| 1map | KET | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.444 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.444 | |
| 3bpz | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | / | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.444 | |
| 1e2k | TMC | Thymidine kinase | / | 0.443 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.443 | |
| 1n5v | NOM | ActVA 6 protein | / | 0.443 | |
| 2vte | IK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.443 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 3p0e | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.443 | |
| 3sop | GDP | Neuronal-specific septin-3 | / | 0.443 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.442 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.442 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.442 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.442 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.442 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 4qx5 | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.442 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 1maq | PGU | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.441 | |
| 1phq | FPE | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.441 | |
| 3e6y | CW1 | 14-3-3-like protein C | / | 0.441 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4l0o | PLP | Cystathionine gamma-synthase | 2.5.1.48 | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 4li8 | 1XQ | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 5k5z | ANP | Uncharacterized protein | / | 0.441 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.440 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.440 | |
| 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 | 0.440 | |
| 4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.440 | |
| 4dya | 0MF | Nucleoprotein | / | 0.440 | |
| 5c7h | NDP | Putative oxidoreductase | / | 0.440 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.440 |