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 |
|---|---|---|---|
| 2br5 | SAH | Cephalosporin hydroxylase CmcI |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 1.000 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.537 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.485 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.483 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.477 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.474 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.473 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.472 | |
| 3zc5 | W9Z | Hepatocyte growth factor receptor | 2.7.10.1 | 0.471 | |
| 4rcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.471 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.471 | |
| 2el0 | SAH | Diphthine synthase | / | 0.470 | |
| 3w8q | AGS | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.470 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.469 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.469 | |
| 1wng | SAH | Diphthine synthase | / | 0.468 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.466 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.466 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.465 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.465 | |
| 2io9 | ADP | Bifunctional glutathionylspermidine synthetase/amidase | / | 0.465 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.465 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.464 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.464 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.464 | |
| 3vw6 | IM6 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.464 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.463 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.462 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.462 | |
| 2z6r | SAH | Diphthine synthase | / | 0.461 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.460 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.460 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.460 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.459 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.459 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1gc5 | ADP | ADP-dependent glucokinase | 2.7.1.147 | 0.457 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.457 | |
| 2dwb | ANP | Aurora kinase A | 2.7.11.1 | 0.457 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.456 | |
| 3zuy | TCH | Transporter | / | 0.456 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 2e4n | SAH | Diphthine synthase | / | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 1dq9 | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.454 | |
| 2e07 | SAH | Diphthine synthase | / | 0.454 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.454 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.453 | |
| 2e16 | SAH | Diphthine synthase | / | 0.453 | |
| 2emr | SAH | Diphthine synthase | / | 0.453 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.453 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 3e8x | NAP | BH1520 protein | / | 0.453 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.453 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.452 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.452 | |
| 1p4a | PCP | Pur operon repressor | / | 0.452 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.452 | |
| 2ejj | SAH | Diphthine synthase | / | 0.452 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2owv | SAH | Diphthine synthase | / | 0.452 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.452 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.452 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.452 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.451 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1y7u | COA | Acyl-CoA hydrolase | / | 0.451 | |
| 2r26 | CMC | Citrate synthase | 2.3.3.16 | 0.451 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.451 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.451 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 2emu | SAH | Diphthine synthase | / | 0.450 | |
| 2hux | SAH | Diphthine synthase | / | 0.450 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.450 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.450 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3pn4 | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.450 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.450 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.449 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.449 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.449 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.449 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.449 | |
| 3cd3 | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.449 | |
| 3wag | TYD | Glycosyltransferase | / | 0.449 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.448 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.448 | |
| 1ml6 | GBX | Glutathione S-transferase A2 | 2.5.1.18 | 0.448 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 2dsg | SAH | Diphthine synthase | / | 0.448 | |
| 2eka | SAH | Diphthine synthase | / | 0.448 | |
| 2en5 | SAH | Diphthine synthase | / | 0.448 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.448 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.448 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.448 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.448 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.448 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.448 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.448 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.447 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.447 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.447 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.447 | |
| 2dxw | SAH | Diphthine synthase | / | 0.447 | |
| 2egb | SAH | Diphthine synthase | / | 0.447 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.447 | |
| 2owk | SAH | Diphthine synthase | / | 0.447 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.447 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.447 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.447 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.447 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.446 | |
| 2huv | SAH | Diphthine synthase | / | 0.446 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.446 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.446 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 3upf | 0BU | Polyprotein | / | 0.446 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.446 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 2c6k | DT2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.445 | |
| 2e8q | SAH | Diphthine synthase | / | 0.445 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.445 | |
| 2hut | SAH | Diphthine synthase | / | 0.445 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.445 | |
| 2pck | SAH | Diphthine synthase | / | 0.445 | |
| 2pzi | AXX | Serine/threonine-protein kinase PknG | 2.7.11.1 | 0.445 | |
| 2ydx | STL | Methionine adenosyltransferase 2 subunit beta | / | 0.445 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4k5p | 1OS | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4ng5 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.444 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.444 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.444 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.444 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.444 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.444 | |
| 4ask | K0I | Lysine-specific demethylase 6B | 1.14.11 | 0.444 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.444 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.444 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.444 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.443 | |
| 2egs | SAH | Diphthine synthase | / | 0.443 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.443 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.443 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.443 | |
| 4l3q | 926 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.442 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 1ix1 | BB2 | Peptide deformylase | / | 0.442 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.442 | |
| 1rkd | ADP | Ribokinase | / | 0.442 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.442 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.442 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.442 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3a62 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.442 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 4e9a | QAP | Peptide deformylase | / | 0.442 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.442 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.442 | |
| 1aj2 | 2PH | Dihydropteroate synthase | / | 0.441 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.441 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1tys | TMP | Thymidylate synthase | / | 0.441 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2b9i | ADP | Mitogen-activated protein kinase FUS3 | 2.7.11.24 | 0.441 | |
| 2dxv | SAH | Diphthine synthase | / | 0.441 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.441 | |
| 2fto | TMP | Thymidylate synthase | / | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.441 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.441 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.441 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.441 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.441 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.440 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.440 | |
| 2fr1 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.440 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.440 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.440 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.440 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.440 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.440 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.440 | |
| 3td7 | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.440 | |
| 5a3c | NAD | SIR2 family protein | / | 0.440 | |
| 5hq8 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.440 |