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 |
|---|---|---|---|
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.826 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.797 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.637 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.611 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.593 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.583 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.582 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.582 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.581 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.578 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.576 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.575 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.572 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.570 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.569 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.559 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.556 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.556 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.553 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.549 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.549 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.536 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.527 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.517 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.507 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.501 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.495 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.493 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.489 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.488 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.486 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.483 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.481 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.479 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.478 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.477 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.476 | |
| 8dfr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.472 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.472 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.470 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.469 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.469 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.469 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.468 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.468 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.466 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.465 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.464 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.464 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.463 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.463 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.462 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.461 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.461 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.460 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.460 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.460 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.459 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.458 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.458 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.457 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.457 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.457 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.456 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.456 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.456 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.455 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.455 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.455 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.454 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.454 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.454 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.452 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.452 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.452 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.452 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.451 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.451 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.451 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.451 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.451 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.451 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.450 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.450 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.450 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.450 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.449 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.449 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.449 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.449 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.448 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.448 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.448 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.448 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.446 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.446 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.446 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4irn | FAD | AnaB | / | 0.446 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.445 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.445 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.444 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.444 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.444 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.444 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.443 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.443 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.443 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.443 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.443 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.442 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.442 | |
| 2p5c | SAH | Diphthine synthase | / | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.441 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.441 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.441 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.440 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.440 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.440 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.440 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.440 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 | |
| 5ftf | ADP | TPR domain protein | / | 0.440 |