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 |
|---|---|---|---|
| 2fme | 3QC | Kinesin-like protein KIF11 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2fme | 3QC | Kinesin-like protein KIF11 | / | 1.000 | |
| 3k5e | K5E | Kinesin-like protein KIF11 | / | 0.640 | |
| 2x7d | EGB | Kinesin-like protein KIF11 | / | 0.620 | |
| 2q2z | MKK | Kinesin-like protein KIF11 | / | 0.617 | |
| 1q0b | NAT | Kinesin-like protein KIF11 | / | 0.606 | |
| 1x88 | NAT | Kinesin-like protein KIF11 | / | 0.604 | |
| 2g1q | N9H | Kinesin-like protein KIF11 | / | 0.599 | |
| 4bbg | V02 | Kinesin-like protein KIF11 | / | 0.595 | |
| 2ieh | MOY | Kinesin-like protein KIF11 | / | 0.593 | |
| 2wog | ZZD | Kinesin-like protein KIF11 | / | 0.589 | |
| 2x2r | X2O | Kinesin-like protein KIF11 | / | 0.586 | |
| 2x7c | KZ9 | Kinesin-like protein KIF11 | / | 0.585 | |
| 2x7e | X7E | Kinesin-like protein KIF11 | / | 0.585 | |
| 3ken | ZZD | Kinesin-like protein KIF11 | / | 0.574 | |
| 2xae | 2XA | Kinesin-like protein KIF11 | / | 0.566 | |
| 2gm1 | 2AZ | Kinesin-like protein KIF11 | / | 0.565 | |
| 4a51 | DQ8 | Kinesin-like protein KIF11 | / | 0.561 | |
| 3k3b | L31 | Kinesin-like protein KIF11 | / | 0.546 | |
| 4a5y | G7X | Kinesin-like protein KIF11 | / | 0.515 | |
| 4as7 | 6LX | Kinesin-like protein KIF11 | / | 0.513 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.497 | |
| 2ye4 | 2FY | Heat shock protein HSP 90-alpha | / | 0.491 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.484 | |
| 3nnu | EDB | Mitogen-activated protein kinase 14 | / | 0.483 | |
| 4asg | 814 | ATP-dependent molecular chaperone HSP82 | / | 0.479 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.470 | |
| 1kfc | IPL | Tryptophan synthase alpha chain | / | 0.469 | |
| 2cdu | FAD | NADH oxidase | / | 0.469 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.468 | |
| 1e8w | QUE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 2wi1 | ZZ2 | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 3amb | VX6 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.467 | |
| 1jg0 | DDT | Thymidylate synthase | / | 0.466 | |
| 2vci | 2GJ | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.465 | |
| 3vfa | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.464 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.464 | |
| 4djq | M86 | Pol polyprotein | / | 0.463 | |
| 3e93 | 19B | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.461 | |
| 1h1p | CMG | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.461 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.461 | |
| 3qx4 | X4B | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.461 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.461 | |
| 1i3m | UD1 | UDP-glucose 4-epimerase | / | 0.460 | |
| 1bcp | ATP | Pertussis toxin subunit 4 | / | 0.459 | |
| 1bcp | ATP | Pertussis toxin subunit 5 | / | 0.459 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.459 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.459 | |
| 2igy | A2T | Plasmepsin 2 | / | 0.459 | |
| 1j1b | ANP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.458 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.458 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.458 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 5e92 | ANP | TGF-beta receptor type-2 | 2.7.11.30 | 0.457 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.456 | |
| 2hs2 | 017 | Protease | / | 0.456 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3w2r | W2R | Epidermal growth factor receptor | 2.7.10.1 | 0.456 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2ydk | YDK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1fvt | 106 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 1j7u | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.454 | |
| 2bxe | 1FL | Serum albumin | / | 0.454 | |
| 3qql | X03 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 3vf7 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1a9m | U0E | Gag-Pol polyprotein | / | 0.453 | |
| 1fej | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 4l45 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.453 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.453 | |
| 1d4y | TPV | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1kv2 | B96 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3ddq | RRC | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1pxp | CK8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 1qcf | PP1 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.451 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.451 | |
| 3lfn | A27 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.451 | |
| 3st5 | G89 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 4acg | 6LQ | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.451 | |
| 4fcq | 2N6 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.450 | |
| 1qiw | DPD | Calmodulin | / | 0.450 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 3fgo | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.450 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.450 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.450 | |
| 1qbs | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2gpv | OHT | Estrogen-related receptor gamma | / | 0.449 | |
| 2xvv | 9DN | Serum albumin | / | 0.449 | |
| 3ezr | EZR | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.449 | |
| 3rpr | 25Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3ugc | 046 | Tyrosine-protein kinase JAK2 | / | 0.449 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.449 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.449 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.448 | |
| 2fdd | 385 | Pol protein | / | 0.448 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 4yqf | GDP | Septin-9 | / | 0.448 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.447 | |
| 1hii | C20 | Gag-Pol polyprotein | / | 0.447 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3lxd | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.447 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.447 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.447 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4hz5 | 19Y | DNA topoisomerase 4 subunit B | / | 0.447 | |
| 3fx5 | KNI | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3qp0 | NI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3rep | ATP | Integrin-linked protein kinase | 2.7.11.1 | 0.446 | |
| 4a2j | AS0 | Progesterone receptor | / | 0.446 | |
| 4egh | 0OY | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.446 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.446 | |
| 1oqc | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.445 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.445 | |
| 1vru | AAP | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 3dol | GWI | Pol protein | / | 0.445 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3qn8 | NI7 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.445 | |
| 1lev | CLI | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.444 | |
| 1meu | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1qbr | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1zsr | 0ZT | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2q63 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2r64 | 740 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3b9l | AZZ | Serum albumin | / | 0.444 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.444 | |
| 3lfq | A28 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 3ndv | AIC | Beta-peptidyl aminopeptidase BapA | / | 0.444 | |
| 3nu9 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4jld | ADP | Adenylate kinase | / | 0.444 | |
| 5djt | FMN | NPH1-2 | / | 0.444 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.444 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.443 | |
| 1qbu | 846 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.443 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.443 | |
| 2eb3 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.443 | |
| 2vu3 | LZE | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2x1n | X1N | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.443 | |
| 5jjr | SAH | Genome polyprotein | / | 0.443 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.442 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 1hpo | UNI | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1hwr | 216 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.442 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2i4x | KGQ | Protease | / | 0.442 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.442 | |
| 3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.442 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.442 | |
| 3s54 | 017 | Protease | / | 0.442 | |
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 4djo | MK5 | Pol polyprotein | / | 0.442 | |
| 4k4p | 3TL | Gag-Pol polyprotein | / | 0.442 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1ody | LP1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.441 | |
| 2p7z | OHT | Estrogen-related receptor gamma | / | 0.441 | |
| 3ekt | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3lit | E15 | Protease | / | 0.441 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.441 | |
| 3mxd | K53 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3rkb | 12Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.441 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1mui | AB1 | Protease | / | 0.440 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2aqu | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2yeg | XQG | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.440 | |
| 3sa9 | A68 | Protease | / | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.440 | |
| 4fsy | HK7 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 4h3z | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.440 |