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 |
|---|---|---|---|
| 2wmd | ZZ0 | NmrA-like family domain-containing protein 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2wmd | ZZ0 | NmrA-like family domain-containing protein 1 | / | 1.000 | |
| 2wm3 | NFL | NmrA-like family domain-containing protein 1 | / | 0.536 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.499 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.482 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.480 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.479 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.478 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.474 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.474 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.473 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.473 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.473 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.473 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.472 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.469 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.469 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.469 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.467 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.467 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.467 | |
| 2bxq | IMN | Serum albumin | / | 0.466 | |
| 3t4h | MD5 | Alpha-ketoglutarate-dependent dioxygenase AlkB | 1.14.11.33 | 0.466 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.462 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.461 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.461 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.461 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3eks | CY9 | Actin-5C | / | 0.460 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.460 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.459 | |
| 3b9l | AZZ | Serum albumin | / | 0.458 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.458 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.457 | |
| 4iil | RBF | Membrane lipoprotein TpN38(b) | / | 0.457 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.456 | |
| 3lxe | TOR | Carbonic anhydrase 1 | 4.2.1.1 | 0.456 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4lcw | 1VY | Major histocompatibility complex class I-related gene protein | / | 0.456 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.455 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.455 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.454 | |
| 2xvw | 9NR | Serum albumin | / | 0.454 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.454 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.454 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.454 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1lke | DOG | Bilin-binding protein | / | 0.453 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.453 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.453 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.453 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.452 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.451 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.451 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.451 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.451 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.450 | |
| 1pl6 | 572 | Sorbitol dehydrogenase | 1.1.1.14 | 0.450 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.450 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.450 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4yu1 | 53N | Aldose reductase | 1.1.1.21 | 0.450 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.450 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3r8h | ZOM | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 1sre | HAB | Streptavidin | / | 0.448 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.448 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.448 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.448 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.448 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1srf | MTB | Streptavidin | / | 0.447 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3ce0 | P34 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.447 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.447 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.447 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.447 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.447 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.447 | |
| 1til | ATP | Anti-sigma F factor | / | 0.446 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 2rtg | BTN | Streptavidin | / | 0.446 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.446 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.446 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.446 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2fhj | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.445 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.445 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.445 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.445 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.444 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.444 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.444 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.444 | |
| 4e2d | FMN | Dehydrogenase | / | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.444 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.444 | |
| 1lcz | BH7 | Streptavidin | / | 0.443 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.443 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.443 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.443 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.443 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.442 | |
| 1srg | MHB | Streptavidin | / | 0.442 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.442 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 1mlz | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 1odn | APV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1sa4 | JAN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1swg | BTN | Streptavidin | / | 0.441 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.441 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 3e33 | ED7 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 1a80 | NDP | 2,5-diketo-D-gluconic acid reductase A | 1.1.1.346 | 0.440 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.440 | |
| 1z89 | 62P | Aldose reductase | 1.1.1.21 | 0.440 | |
| 2iu8 | UD1 | UDP-3-O-acylglucosamine N-acyltransferase | 2.3.1 | 0.440 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.440 | |
| 2r8o | T5X | Transketolase 1 | / | 0.440 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.440 |