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 |
|---|---|---|---|
| 2iwe | 2IH | Azurin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2iwe | 2IH | Azurin | / | 1.000 | |
| 3v8t | 477 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.488 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.487 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.480 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.478 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.476 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.474 | |
| 2lf1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.472 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.471 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.471 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.471 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.471 | |
| 3eku | CY9 | Actin-5C | / | 0.471 | |
| 4cfa | WOP | Integrase | / | 0.471 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.470 | |
| 3i59 | N6S | CRP-like cAMP-activated global transcriptional regulator | / | 0.469 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.468 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.467 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.467 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 4fnz | NZF | ALK tyrosine kinase receptor | 2.7.10.1 | 0.467 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.467 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.466 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.466 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.466 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.465 | |
| 4l98 | LRG | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.465 | |
| 1ahi | CHO | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.463 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.463 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.463 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.462 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.462 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.461 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.459 | |
| 5epo | TUD | 7-alpha-hydroxysteroid deydrogenase | / | 0.459 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.458 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.457 | |
| 2ejj | SAH | Diphthine synthase | / | 0.457 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.457 | |
| 3myk | BIT | Myosin-2 heavy chain | / | 0.457 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.457 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.456 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 4cf8 | V7H | Integrase | / | 0.456 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.456 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.455 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.455 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.455 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.455 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.455 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.454 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.454 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.454 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.453 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 2gfd | RDA | Endoplasmin | / | 0.452 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.452 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1sr7 | MOF | Progesterone receptor | / | 0.451 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.451 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.451 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 2hek | GDP | Uncharacterized protein | / | 0.451 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.451 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.451 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.451 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.451 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.451 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.450 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.450 | |
| 2bxo | OPB | Serum albumin | / | 0.450 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3wec | AUI | Cytochrome P450 | / | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.449 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.449 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 4pzt | SOP | Histone acetyltransferase p300 | / | 0.449 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.448 | |
| 1tys | DHF | Thymidylate synthase | / | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.448 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.448 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.448 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.448 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.448 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.447 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.447 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.447 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.447 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.447 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.447 | |
| 4ces | NFW | Integrase | / | 0.447 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.446 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4ceo | G0T | Integrase | / | 0.446 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.446 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 4ubt | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.446 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.445 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.445 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.445 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.445 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.445 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.445 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.445 | |
| 3i68 | J4Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.445 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.445 | |
| 4b1f | KRH | Glutamate racemase | / | 0.445 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.445 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.444 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.444 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.444 | |
| 2e16 | SAH | Diphthine synthase | / | 0.444 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.444 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.444 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.443 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.443 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3kq7 | KQ7 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3nks | ACJ | Protoporphyrinogen oxidase | 1.3.3.4 | 0.443 | |
| 3pgt | GBX | Glutathione S-transferase P | 2.5.1.18 | 0.443 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.443 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.443 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.442 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.442 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.442 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.442 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.442 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.442 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3stx | BKA | Methylketone synthase I | / | 0.442 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.442 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.441 | |
| 1t57 | FMN | Conserved protein | / | 0.441 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.441 | |
| 4i7f | NVE | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.441 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.441 | |
| 5doz | NDP | JamJ | / | 0.441 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.440 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1pgt | GTX | Glutathione S-transferase P | 2.5.1.18 | 0.440 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.440 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2hps | CTZ | Ca2+-triggered coelenterazine-binding protein 1 | / | 0.440 | |
| 2y3s | TIR | TamL | / | 0.440 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.440 | |
| 3i1f | GCP | Translation initiation factor 2 subunit gamma | / | 0.440 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.440 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4aot | GW8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.440 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.440 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.440 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.440 |