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 |
|---|---|---|---|
| 3rc9 | TLO | Sugar 3-ketoreductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3rc9 | TLO | Sugar 3-ketoreductase | / | 1.000 | |
| 3rc7 | TLO | Sugar 3-ketoreductase | / | 0.527 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.493 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.487 | |
| 3cv7 | C2U | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 | 0.486 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.484 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.480 | |
| 1enp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.479 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.479 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.479 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.478 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.477 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.476 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.473 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.472 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.472 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.471 | |
| 2c6c | 24I | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.471 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.470 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.469 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.469 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.469 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.468 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.468 | |
| 4g8c | C6L | Alpha/beta hydrolase fold protein | / | 0.468 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.468 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.467 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.467 | |
| 1f9a | ATP | Nicotinamide-nucleotide adenylyltransferase | / | 0.466 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 2x0e | TYD | WsaF | / | 0.466 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.466 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.466 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.465 | |
| 4b8z | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.465 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.465 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.465 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.465 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.464 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.464 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.464 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.464 | |
| 4ffm | ADP | Uncharacterized protein | / | 0.464 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.464 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.463 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.463 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.463 | |
| 4kq2 | 1S3 | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.463 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.462 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.462 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.462 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.462 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.462 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.461 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.461 | |
| 4uyg | 73B | Bromodomain-containing protein 2 | / | 0.461 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.461 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.460 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.460 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.460 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.459 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.459 | |
| 2wwj | Y28 | Lysine-specific demethylase 4A | / | 0.459 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.459 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.459 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.459 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.459 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.458 | |
| 1g4p | FQP | Thiamine-phosphate synthase | / | 0.458 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.458 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.458 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.458 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.458 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.458 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.457 | |
| 4bl5 | GFB | GDP-L-fucose synthase | 1.1.1.271 | 0.457 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.457 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.456 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.456 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.456 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.456 | |
| 3chs | 4BU | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.456 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.456 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.456 | |
| 1y6q | TDI | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 3.2.2.9 | 0.455 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.455 | |
| 2o4g | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.455 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.455 | |
| 3pz3 | PZ3 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.455 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.454 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.454 | |
| 3u5s | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.454 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.453 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.453 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.453 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.452 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.452 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.452 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.452 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 1m67 | BOA | Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal | 1.1.1.8 | 0.451 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.451 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.451 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.451 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.451 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.451 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4mry | CEI | Obelin | / | 0.451 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.451 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.450 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.450 | |
| 2vqj | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.450 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.450 | |
| 1vft | DCS | Alanine racemase | / | 0.449 | |
| 2qjp | ANJ | Cytochrome b | / | 0.449 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.449 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.449 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.449 | |
| 5kf2 | COA | Predicted acetyltransferase | / | 0.449 | |
| 1iay | AVG | 1-aminocyclopropane-1-carboxylate synthase 2 | 4.4.1.14 | 0.448 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.448 | |
| 1n08 | ADP | Riboflavin kinase | 2.7.1.26 | 0.448 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.448 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.448 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.448 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.448 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.447 | |
| 1odn | APV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2piw | DHT | Androgen receptor | / | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3o8g | O8G | HTH-type transcriptional regulator EthR | / | 0.447 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2fzb | TOL | Aldose reductase | 1.1.1.21 | 0.446 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.446 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.446 | |
| 3up3 | XCA | aceDAF-12 | / | 0.446 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.446 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.446 | |
| 4yfy | 1YJ | VioF | / | 0.446 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.445 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 1uze | EAL | Angiotensin-converting enzyme | 3.2.1 | 0.445 | |
| 1xjq | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.445 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.445 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.445 | |
| 2wgs | 1AZ | Glutamine synthetase | 6.3.1.2 | 0.445 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.445 | |
| 3bsy | ACO | UDP-N-acetylbacillosamine N-acetyltransferase | 2.3.1.203 | 0.445 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.445 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.445 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.445 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.445 | |
| 4bqw | QNM | Egl nine homolog 1 | / | 0.445 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.445 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.445 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.444 | |
| 1g0r | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.444 | |
| 1yrx | FMN | AppA protein | / | 0.444 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2o3u | NGD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.444 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.444 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.444 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.444 | |
| 4aoa | IK2 | Beta-phenylalanine transaminase | 2.6.1 | 0.444 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.444 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.443 | |
| 2pit | DHT | Androgen receptor | / | 0.443 | |
| 3ghh | 2NF | CD38 molecule | / | 0.443 | |
| 3gyf | 51P | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4blc | NDP | Catalase | 1.11.1.6 | 0.443 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.442 | |
| 1rp4 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.442 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.442 | |
| 4g8b | HL6 | Alpha/beta hydrolase fold protein | / | 0.442 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4xul | GTP | Uncharacterized protein mg662 | / | 0.442 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.441 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.441 | |
| 1zos | MTM | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | / | 0.441 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.441 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.441 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.441 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4kxj | P34 | Nucleoprotein | / | 0.441 | |
| 3p0g | P0G | Beta-2 adrenergic receptor | / | 0.441 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.440 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 2iyp | A2P | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.440 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.440 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.440 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 2yhu | WHF | Pteridine reductase | / | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.440 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4eh5 | IRG | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4jhi | EMU | Nodulin-13 | / | 0.440 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |