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 |
|---|---|---|---|
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 1.000 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.625 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.612 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.590 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.583 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.575 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.569 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.552 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.533 | |
| 2w14 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.529 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.517 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.508 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.506 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.505 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.494 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.493 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.491 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.479 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.477 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.476 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.476 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.475 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.475 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.473 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.473 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.473 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.471 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.471 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.469 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.469 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.467 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.466 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.465 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.464 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 2pam | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.463 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.463 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.463 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.461 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.461 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.459 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.458 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.458 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.457 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.457 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.457 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.456 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.456 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.456 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.455 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.455 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.455 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.455 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.455 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 1j1b | ANP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.454 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.454 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.454 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.454 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.454 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.454 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.454 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.454 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2y4g | TIR | TamL | / | 0.453 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 4qna | X11 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.453 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.452 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.452 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.452 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.452 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.452 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.452 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.451 | |
| 3bmo | NAP | Pteridine reductase | / | 0.451 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.450 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.450 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.450 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.449 | |
| 3vgl | ANP | Glucokinase | / | 0.449 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.449 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.448 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.448 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.448 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.448 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.448 | |
| 4gi5 | FAD | Putative NAD(P)H dehydrogenase (Quinone) | / | 0.448 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.448 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.448 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.447 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.447 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.447 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.447 | |
| 5ftf | ADP | TPR domain protein | / | 0.447 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.446 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.446 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.446 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.445 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.445 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.445 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 6gsw | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.445 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.444 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.444 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.444 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3kds | NHX | ATP-dependent zinc metalloprotease FtsH | / | 0.444 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.444 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.444 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.443 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.443 | |
| 1ohh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1ohh | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.443 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.443 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4g73 | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.443 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.442 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.442 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 2wqp | WQP | Polysialic acid capsule biosynthesis protein SiaC | / | 0.442 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.442 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.442 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.442 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.442 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2gd6 | ACO | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.441 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.441 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.440 | |
| 1jmh | UMP | Thymidylate synthase | / | 0.440 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.440 | |
| 2gst | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.440 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.440 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.440 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.440 |