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 |
|---|---|---|---|
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 1.000 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.685 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.610 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.515 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.511 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.509 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.508 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.503 | |
| 1y7t | NDP | Malate dehydrogenase | / | 0.498 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.496 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.491 | |
| 3ieu | GDP | GTPase Era | / | 0.485 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.484 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.482 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.476 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.476 | |
| 3a3g | DLZ | Lumazine protein | / | 0.475 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.474 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.473 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.472 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.471 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.471 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.470 | |
| 1wzi | NDP | Malate dehydrogenase | / | 0.470 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.469 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.469 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.469 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.468 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.468 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.467 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.467 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.467 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.466 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.465 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.465 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.465 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.464 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.464 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.464 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.463 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.462 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.461 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.461 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.460 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.459 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.458 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.458 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.458 | |
| 2y4g | TIR | TamL | / | 0.458 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.458 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.458 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.458 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.457 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.457 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.456 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.456 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.455 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.455 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.455 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 2y3s | TIR | TamL | / | 0.454 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.454 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.454 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.454 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.453 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.453 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3r4b | 74T | Gag-Pol polyprotein | / | 0.453 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.452 | |
| 3iaa | TYD | CalG2 | / | 0.452 | |
| 3wag | TYD | Glycosyltransferase | / | 0.452 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.451 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.451 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.451 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.451 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.451 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 4h1v | GNP | Dynamin-1-like protein | 3.6.5.5 | 0.451 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.450 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.450 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.450 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.450 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.450 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.450 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.450 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.450 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 1b8u | NAD | Malate dehydrogenase | / | 0.448 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.448 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.448 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.448 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.448 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 1iy8 | NAD | Levodione reductase | / | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.446 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.446 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.446 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.446 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.445 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.445 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.445 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.445 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.444 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.444 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 4de0 | 0JB | Beta-lactamase | / | 0.443 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.443 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.442 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.442 | |
| 2p3b | 3TL | V-1 protease | / | 0.442 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.442 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 4ejv | LCL | Transcriptional regulator TcaR | / | 0.441 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.441 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.441 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.441 | |
| 1gv0 | NAD | Malate dehydrogenase | / | 0.440 | |
| 3r95 | ACO | MccE protein | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.440 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.440 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.440 |