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 |
|---|---|---|---|
| 4gnc | ASO | Regucalcin | 3.1.1.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 1.000 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.496 | |
| 4l9q | 9TP | Serum albumin | / | 0.492 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.486 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.486 | |
| 4yaf | 2AM | NADPH--cytochrome P450 reductase | / | 0.475 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.474 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.472 | |
| 4yau | 2AM | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.472 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.471 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.471 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.469 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.468 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.467 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.462 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.462 | |
| 3qfc | NAP | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 1x8v | ESL | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.461 | |
| 2bxo | OPB | Serum albumin | / | 0.461 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.461 | |
| 2wb2 | FAD | RE11660p | / | 0.461 | |
| 2y3r | TRK | TamL | / | 0.461 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.460 | |
| 3gue | UPG | UTP-glucose-1-phosphate uridylyltransferase 2, putative | / | 0.460 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.460 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.460 | |
| 2wq6 | FAD | RE11660p | / | 0.459 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.459 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.459 | |
| 3qfs | NAP | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.458 | |
| 3sop | GDP | Neuronal-specific septin-3 | / | 0.457 | |
| 4yal | 2AM | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.456 | |
| 2vax | CSC | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.456 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.456 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.456 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.456 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.455 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.454 | |
| 1amo | NAP | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.453 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.453 | |
| 4zse | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.453 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.453 | |
| 2hw1 | ANP | Ketohexokinase | / | 0.452 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.452 | |
| 4iak | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.451 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.451 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4y7c | NAP | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.451 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.450 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.450 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.449 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.449 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.449 | |
| 4f99 | ADP | Cell division cycle 7-related protein kinase | 2.7.11.1 | 0.449 | |
| 4iah | 1DX | Alr2278 protein | / | 0.449 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.449 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.449 | |
| 1eio | GCH | Gastrotropin | / | 0.448 | |
| 1qxo | FMN | Chorismate synthase | / | 0.448 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.448 | |
| 3cvu | FAD | RE11660p | / | 0.448 | |
| 3h23 | B54 | Dihydropteroate synthase | / | 0.448 | |
| 3zlm | ANP | Adenosine monophosphate-protein transferase NmFic | 2.7.7.n1 | 0.448 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.448 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1lhw | ESM | Sex hormone-binding globulin | / | 0.447 | |
| 1owo | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.447 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.447 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.447 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.447 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.447 | |
| 1ja1 | NAP | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.446 | |
| 2ga9 | AGS | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.446 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.446 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.446 | |
| 3qe2 | NAP | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.446 | |
| 4g3q | UD1 | Bifunctional protein GlmU | / | 0.446 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.446 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.445 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.445 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 2y3r | TIR | TamL | / | 0.445 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4l8u | 9AZ | Serum albumin | / | 0.445 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.444 | |
| 1tae | NAD | DNA ligase | / | 0.444 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.444 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.444 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4hdg | GTP | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 3gd3 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.443 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.443 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.443 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.442 | |
| 2aaz | CB3 | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.442 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.442 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2rc3 | NAD | CBS domain | / | 0.441 | |
| 3af2 | ACP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.441 | |
| 4fxf | ATP | Pyruvate kinase PKM | 2.7.1.40 | 0.441 | |
| 4zm3 | PLP | Aminotransferase | / | 0.441 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.440 | |
| 1own | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.440 | |
| 3fgo | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.440 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 4jrn | ANP | Rhoptry kinase family protein | / | 0.440 |