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 |
|---|---|---|---|
| 2ji5 | UTP | Uridylate kinase | 2.7.4.22 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ji5 | UTP | Uridylate kinase | 2.7.4.22 | 1.000 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.500 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.491 | |
| 1gqt | ACP | Ribokinase | / | 0.488 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.486 | |
| 2j4k | U5P | Uridylate kinase | 2.7.4.22 | 0.485 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.482 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.482 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.475 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.474 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.473 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.473 | |
| 1r2j | FAD | FkbI | / | 0.471 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.471 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.469 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.466 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.465 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.465 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.464 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.463 | |
| 3arv | SAU | Chitinase A | / | 0.463 | |
| 4jic | FMN | GTN Reductase | / | 0.463 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.462 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.462 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.461 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.461 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.461 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.460 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.460 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.460 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.459 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.458 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.458 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2j4l | UTP | Uridylate kinase | 2.7.4.22 | 0.457 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.457 | |
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.457 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.456 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.456 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.455 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.455 | |
| 3ama | SKE | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.454 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.454 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.453 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.452 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 4zol | ACP | Tubulin tyrosine ligase | / | 0.452 | |
| 1tqm | ANP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.451 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.451 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.450 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.450 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.450 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.450 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.450 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.449 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4oh4 | ANP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.449 | |
| 4p63 | NAD | Probable deoxyhypusine synthase | 2.5.1.46 | 0.449 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.448 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.448 | |
| 2rl2 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.448 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.447 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.447 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.447 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.447 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.447 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.447 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.447 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 4rfl | NDP | Glycerol-1-phosphate dehydrogenase [NAD(P)+] | / | 0.447 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.447 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.447 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.447 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.446 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.446 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.446 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.446 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.446 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.445 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.445 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.445 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.444 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.444 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.444 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.444 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.443 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.443 | |
| 2yw2 | ATP | Phosphoribosylamine--glycine ligase | / | 0.443 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3gst | GPR | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.443 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.443 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.443 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.442 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.442 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.442 | |
| 1djn | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.441 | |
| 1jq5 | NAD | Glycerol dehydrogenase | 1.1.1.6 | 0.441 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.440 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 | |
| 4uck | SAM | Large structural protein | / | 0.440 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 |