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 |
|---|---|---|---|
| 1sbz | FMN | Probable UbiX-like flavin prenyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1sbz | FMN | Probable UbiX-like flavin prenyltransferase | / | 1.000 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.487 | |
| 3pn1 | IVH | DNA ligase | / | 0.483 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.482 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.481 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.480 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.479 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.479 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 1ddu | DDU | Thymidylate synthase | / | 0.477 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.477 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.475 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.475 | |
| 2hzq | STR | Apolipoprotein D | / | 0.474 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.474 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.472 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.472 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.471 | |
| 3lpg | Z78 | Beta-glucuronidase | 3.2.1.31 | 0.471 | |
| 4fou | C2E | Uncharacterized protein | / | 0.471 | |
| 2zi6 | 3D1 | Deoxycytidine kinase | 2.7.1.74 | 0.470 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.469 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.469 | |
| 4itx | IN5 | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.469 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.468 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.468 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.467 | |
| 4bue | JQF | Tankyrase-2 | 2.4.2.30 | 0.467 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.466 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.466 | |
| 4m2b | UPG | UDP-glucose pyrophosphorylase | / | 0.466 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.465 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.465 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.465 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.465 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.464 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.464 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.464 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.463 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.463 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.462 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.462 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.461 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.461 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.461 | |
| 5fe1 | 12Q | Histone acetyltransferase KAT2B | 2.3.1.48 | 0.461 | |
| 2z4w | 749 | Geranylgeranyl pyrophosphate synthase | / | 0.460 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.460 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.460 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.459 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.459 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.457 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.457 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.456 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.455 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.455 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.454 | |
| 3ox2 | 79X | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.454 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.454 | |
| 4cw5 | FMN | DfnA | / | 0.454 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.453 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4kzl | 20D | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.453 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.453 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.452 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 5doz | NDP | JamJ | / | 0.452 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.451 | |
| 1jf0 | CZH | Obelin | / | 0.451 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.451 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.451 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1gp6 | QUE | Leucoanthocyanidin dioxygenase | 1.14.11.19 | 0.450 | |
| 1re0 | AFB | ADP-ribosylation factor 1 | / | 0.450 | |
| 1re0 | AFB | ARF guanine-nucleotide exchange factor 1 | / | 0.450 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.450 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4lh7 | 1X8 | DNA ligase | / | 0.450 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.450 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.449 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.449 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1r4l | XX5 | Angiotensin-converting enzyme 2 | 3.4.17.23 | 0.448 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.448 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.448 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.448 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.448 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.447 | |
| 3ceh | AVE | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.447 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.447 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.447 | |
| 4dq1 | UMP | Thymidylate synthase | / | 0.447 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 1pgt | GTX | Glutathione S-transferase P | 2.5.1.18 | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 1u33 | LM2 | Pancreatic alpha-amylase | / | 0.446 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.446 | |
| 2hp2 | KE4 | Glutamate-1-semialdehyde 2,1-aminomutase | 5.4.3.8 | 0.446 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.446 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.446 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.446 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.445 | |
| 1cne | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.445 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1qr2 | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.445 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.445 | |
| 3e7i | B2 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.445 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.444 | |
| 2wwj | Y28 | Lysine-specific demethylase 4A | / | 0.444 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 5fsi | 8DG | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.444 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.443 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.443 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.443 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.443 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.443 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.443 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 2g89 | UMP | Thymidylate synthase | / | 0.442 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.442 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.442 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.442 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1el4 | CTZ | Obelin | / | 0.441 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.441 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.441 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3ox1 | 695 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.441 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.441 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.441 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3lm1 | LEC | Agglutinin alpha chain | / | 0.440 | |
| 3nfr | EWQ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 3nhp | HGZ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.440 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.440 |