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 |
|---|---|---|---|
| 4mfe | BTN | Pyruvate carboxylase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4mfe | BTN | Pyruvate carboxylase | / | 1.000 | |
| 4loc | BTN | Pyruvate carboxylase | / | 0.703 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.531 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.516 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.504 | |
| 4g2g | TDH | Mycocyclosin synthase | 1.14.21.9 | 0.493 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.488 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.484 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.480 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.474 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.473 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.472 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.469 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.468 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.465 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.465 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.464 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.464 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.463 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.463 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.462 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.460 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.458 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.458 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.458 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.456 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.456 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.456 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.456 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.456 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.455 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.454 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.454 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.453 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.451 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.451 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.451 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.451 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.451 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.450 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.450 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.449 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.449 | |
| 1ppj | ANY | Cytochrome b | / | 0.448 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 3eks | CY9 | Actin-5C | / | 0.448 | |
| 3iex | GMP | Purine nucleoside phosphorylase | / | 0.448 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.448 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.448 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.447 | |
| 2qir | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.447 | |
| 2zrj | AGS | Protein RecA | / | 0.447 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.447 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.447 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.447 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.447 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.446 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.446 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.446 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 5e7o | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.446 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.444 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.444 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.444 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.444 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4pd6 | URI | Nucleoside permease | / | 0.444 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1mfz | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.443 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1sve | I01 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.443 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.443 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.443 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.443 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.443 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.443 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.443 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.443 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3c1o | NAP | Eugenol synthase | / | 0.442 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.442 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.442 | |
| 3r96 | ACO | MccE protein | / | 0.442 | |
| 4de0 | 0JB | Beta-lactamase | / | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.441 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 2rm2 | W43 | Genome polyprotein | / | 0.441 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.441 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 4f97 | VDO | Putative glycosyltransferase | / | 0.441 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.441 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.440 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 1vbn | YSA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.440 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.440 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.440 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.440 |