sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1fm8 | DDC | Chalcone--flavonone isomerase 1 | 5.5.1.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1fm8 | DDC | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 1.000 | |
| 1eyq | NAR | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.597 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.585 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.493 | |
| 4l9q | 9TP | Serum albumin | / | 0.492 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.477 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.475 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 2ya3 | J7V | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.473 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.470 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.470 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.469 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.469 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.468 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.467 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.467 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.466 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.466 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.465 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.465 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.465 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.464 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.464 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.462 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.461 | |
| 3qce | NXY | Receptor-type tyrosine-protein phosphatase gamma | 3.1.3.48 | 0.461 | |
| 2axn | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | / | 0.459 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.459 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3lu8 | IQX | Serum albumin | / | 0.459 | |
| 4iqk | IQK | Kelch-like ECH-associated protein 1 | / | 0.459 | |
| 4v12 | POG | MaoC like domain protein | / | 0.459 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.459 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.458 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.458 | |
| 1gq2 | NAP | NADP-dependent malic enzyme | 1.1.1.40 | 0.457 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.457 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.457 | |
| 3vs2 | VSB | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.457 | |
| 4o3m | ADP | Bloom syndrome protein | 3.6.4.12 | 0.457 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.456 | |
| 3af2 | ACP | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.455 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.455 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 1jx0 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.454 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.454 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.454 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 2z78 | H86 | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.454 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.454 | |
| 1qmg | APX | Ketol-acid reductoisomerase, chloroplastic | 1.1.1.86 | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3vrz | VRZ | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.453 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.453 | |
| 4l9k | EHF | Serum albumin | / | 0.453 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.452 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.452 | |
| 2y3r | TRK | TamL | / | 0.452 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.452 | |
| 3m31 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.452 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.452 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.451 | |
| 2dbz | NAP | Glyoxylate reductase | 1.1.1.26 | 0.451 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.451 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3lnv | 1ZZ | Saframycin Mx1 synthetase B | / | 0.451 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.451 | |
| 4cnz | ADP | Nitrogen regulatory protein P-II 1 | / | 0.451 | |
| 4ifn | 12O | Kelch-like ECH-associated protein 1 | / | 0.451 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2hps | CTZ | Ca2+-triggered coelenterazine-binding protein 1 | / | 0.450 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.450 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3vs0 | VS0 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.450 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.450 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.450 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.449 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.449 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.449 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.449 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.449 | |
| 3qqs | 17C | Anthranilate phosphoribosyltransferase | / | 0.449 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.449 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.449 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.448 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.448 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1v3s | ATP | Signaling protein | / | 0.448 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.448 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.448 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.448 | |
| 3fgo | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.448 | |
| 3h18 | PMS | Esterase/lipase | / | 0.448 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.448 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.448 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.448 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.448 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.447 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.447 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2nom | DUT | Poly(A) polymerase, putative | / | 0.447 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.447 | |
| 2y3s | TIR | TamL | / | 0.447 | |
| 2y4g | TIR | TamL | / | 0.447 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.447 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.446 | |
| 1w87 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 2a41 | ATP | Actin, alpha skeletal muscle | / | 0.446 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3ocp | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.446 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.446 | |
| 2j4z | 626 | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2y30 | SM8 | Putative repressor SimReg2 | / | 0.445 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.445 | |
| 3ntg | D72 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.445 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.445 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 1j7u | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.444 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.444 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2aaz | CB3 | Thymidylate synthase | 2.1.1.45 | 0.444 | |
| 2bxi | AZQ | Serum albumin | / | 0.444 | |
| 2c9e | PID | Peridinin-chlorophyll a protein, high-salt form | / | 0.444 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.444 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.444 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.444 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.444 | |
| 3qck | NX5 | Receptor-type tyrosine-protein phosphatase gamma | 3.1.3.48 | 0.444 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.444 | |
| 4dee | ADP | Aurora kinase A | 2.7.11.1 | 0.444 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.444 | |
| 4fk1 | FAD | Putative thioredoxin reductase | / | 0.444 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4jbq | VX6 | Aurora kinase A | 2.7.11.1 | 0.444 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.444 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.444 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.444 | |
| 1ju6 | LYA | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.443 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.443 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3ncr | ADP | Nitrogen regulatory protein P-II (GlnB-2) | / | 0.443 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.443 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.443 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.442 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.442 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.442 | |
| 2oby | NAP | Quinone oxidoreductase PIG3 | 1 | 0.442 | |
| 2xvv | 9DN | Serum albumin | / | 0.442 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.442 | |
| 3ncq | ATP | Nitrogen regulatory protein P-II (GlnB-2) | / | 0.442 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.442 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.441 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.441 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.441 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.441 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.441 | |
| 3gob | HXX | DdmC | / | 0.441 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.441 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 3tlk | EB4 | Ferrienterobactin-binding periplasmic protein | / | 0.441 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.441 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.441 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.441 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1cx4 | CMP | cAMP-dependent protein kinase type II-beta regulatory subunit | / | 0.440 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1qcf | PP1 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.440 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.440 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.440 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.440 | |
| 3kdu | NKS | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 3lf0 | ATP | Nitrogen regulatory protein P-II | / | 0.440 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.440 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.440 | |
| 3oct | 1N1 | Tyrosine-protein kinase BTK | 2.7.10.2 | 0.440 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.440 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.440 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.440 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.440 |