sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 1.000 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.704 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.493 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.492 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.487 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.485 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.484 | |
| 5dp2 | NAP | CurF | / | 0.482 | |
| 3e8x | NAP | BH1520 protein | / | 0.480 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.480 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.479 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.475 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.472 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.471 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.471 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.467 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.461 | |
| 2xvv | 9DN | Serum albumin | / | 0.460 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.459 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.459 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.459 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.458 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.456 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.456 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.455 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.455 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.455 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.454 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.453 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.453 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 1pwu | GM6 | Lethal factor | 3.4.24.83 | 0.452 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.452 | |
| 3keq | NAD | Redox-sensing transcriptional repressor Rex | / | 0.452 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.452 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2xvw | 9NR | Serum albumin | / | 0.451 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.450 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.449 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.449 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.448 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.448 | |
| 4lb2 | DM5 | Serum albumin | / | 0.448 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.447 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.446 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.446 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.445 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.445 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.445 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.445 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.445 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 2fhk | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.442 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.442 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.441 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.441 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.440 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.440 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.440 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.440 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 |