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 |
|---|---|---|---|
| 1lru | BB2 | Peptide deformylase | 3.5.1.88 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1lru | BB2 | Peptide deformylase | 3.5.1.88 | 1.000 | |
| 1g2a | BB2 | Peptide deformylase | 3.5.1.88 | 0.647 | |
| 1g27 | BB1 | Peptide deformylase | 3.5.1.88 | 0.624 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.561 | |
| 4wxl | BB2 | Peptide deformylase | / | 0.541 | |
| 3pn4 | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.533 | |
| 1ix1 | BB2 | Peptide deformylase | / | 0.506 | |
| 3m6p | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.503 | |
| 3u04 | BB2 | Peptide deformylase | / | 0.499 | |
| 4e9a | QAP | Peptide deformylase | / | 0.494 | |
| 3o3j | BB4 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.490 | |
| 2ew5 | Y12 | Peptide deformylase | / | 0.489 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.484 | |
| 1ws1 | BB2 | Peptide deformylase 1 | / | 0.482 | |
| 4je7 | BB2 | Peptide deformylase 1A, chloroplastic/mitochondrial | 3.5.1.88 | 0.480 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.478 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.474 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.473 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.473 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.473 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.470 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.468 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.468 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.468 | |
| 5cyo | GDP | Septin-9 | / | 0.468 | |
| 3e3u | NVC | Peptide deformylase | 3.5.1.88 | 0.467 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.467 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.466 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.466 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.466 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.466 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.466 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.465 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.465 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.464 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.463 | |
| 3u7k | MDB | Peptide deformylase | / | 0.463 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.462 | |
| 3zkb | ANP | DNA gyrase subunit B | / | 0.462 | |
| 5ej5 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.462 | |
| 1aj8 | COA | Citrate synthase | / | 0.461 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.461 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.461 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.461 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.460 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.460 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.460 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.460 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.459 | |
| 4e9b | BB2 | Peptide deformylase | / | 0.459 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.459 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.458 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.458 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.458 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.458 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.457 | |
| 4bls | APC | NTPase P4 | / | 0.457 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.457 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.457 | |
| 4qxp | 1YE | Stimulator of interferon genes protein | / | 0.457 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.457 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.456 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.456 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.456 | |
| 2os3 | BB2 | Peptide deformylase | / | 0.456 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.455 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.455 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.455 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.454 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.454 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.454 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.454 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4qxr | 1YE | Stimulator of interferon genes protein | / | 0.454 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.453 | |
| 2ew6 | Y13 | Peptide deformylase | / | 0.453 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.453 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.453 | |
| 1y5x | E89 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.452 | |
| 3nks | ACJ | Protoporphyrinogen oxidase | 1.3.3.4 | 0.452 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.452 | |
| 4hi0 | GDP | Urease accessory protein UreG | / | 0.452 | |
| 2bbw | GP5 | Adenylate kinase 4, mitochondrial | / | 0.451 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.451 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.450 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.450 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.450 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 4biz | ADP | Sensor histidine kinase CpxA | / | 0.450 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.450 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.450 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.449 | |
| 1lry | BB2 | Peptide deformylase | / | 0.449 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 2wq6 | FAD | RE11660p | / | 0.449 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.449 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.449 | |
| 4jxr | ACO | Acetyltransferase | / | 0.449 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.449 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.449 | |
| 1kh2 | ATP | Argininosuccinate synthase | / | 0.448 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.448 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 3c4z | ADP | Rhodopsin kinase | / | 0.448 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.448 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.448 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.448 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 1v1b | ATP | 2-dehydro-3-deoxygluconokinase | 2.7.1.45 | 0.447 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3c50 | ADP | Rhodopsin kinase | / | 0.447 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3uwb | BB2 | RIIA-RIIB membrane-associated protein | / | 0.447 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.447 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.447 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.447 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.447 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.446 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.446 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.446 | |
| 3b9l | AZZ | Serum albumin | / | 0.446 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.446 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.446 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.446 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2aia | SB8 | Peptide deformylase | / | 0.445 | |
| 2bkk | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.445 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.445 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.445 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.445 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.445 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.445 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.445 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.445 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.444 | |
| 1rl4 | BRR | Peptide deformylase | / | 0.444 | |
| 2rio | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.444 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.444 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3td7 | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.443 | |
| 4iak | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4jlo | ADP | Adenylate kinase | / | 0.443 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.443 | |
| 4qxq | 1YE | Stimulator of interferon genes protein | / | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.442 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3svj | 4LI | Peptide deformylase | / | 0.442 | |
| 4z38 | FMN | MlnA | / | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.442 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.441 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.441 | |
| 2owk | SAH | Diphthine synthase | / | 0.441 | |
| 2q3e | NAI | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.441 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.441 | |
| 3csc | ACO | Citrate synthase, mitochondrial | 2.3.3.1 | 0.441 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.441 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.441 | |
| 4jld | ADP | Adenylate kinase | / | 0.441 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.441 | |
| 2pch | SAH | Diphthine synthase | / | 0.440 | |
| 2r26 | CMC | Citrate synthase | 2.3.3.16 | 0.440 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.440 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.440 | |
| 3nbv | ANP | Ketohexokinase | / | 0.440 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.440 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 5ftc | ADP | TPR domain protein | / | 0.440 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.440 |