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 |
|---|---|---|---|
| 4fx2 | FMN | Flavodoxin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fx2 | FMN | Flavodoxin | / | 1.000 | |
| 1fx1 | FMN | Flavodoxin | / | 0.722 | |
| 1j9g | FMN | Flavodoxin | / | 0.607 | |
| 1bu5 | RBF | Flavodoxin | / | 0.596 | |
| 5fx2 | FMN | Flavodoxin | / | 0.593 | |
| 1azl | FMN | Flavodoxin | / | 0.590 | |
| 3f6r | FMN | Flavodoxin | / | 0.586 | |
| 2fx2 | FMN | Flavodoxin | / | 0.580 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.574 | |
| 1aku | FMN | Flavodoxin | / | 0.561 | |
| 1wsb | FMN | Flavodoxin | / | 0.549 | |
| 1xyv | FMN | Flavodoxin | / | 0.543 | |
| 3f6s | FMN | Flavodoxin | / | 0.541 | |
| 1j8q | FMN | Flavodoxin | / | 0.538 | |
| 1akr | FMN | Flavodoxin | / | 0.537 | |
| 1c7f | FMN | Flavodoxin | / | 0.528 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.524 | |
| 1akw | FMN | Flavodoxin | / | 0.522 | |
| 3kaq | FMN | Flavodoxin | / | 0.515 | |
| 3kap | FMN | Flavodoxin | / | 0.512 | |
| 3f90 | FMN | Flavodoxin | / | 0.511 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.508 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.502 | |
| 5xr8 | FMN | Cannabinoid receptor 1 | / | 0.502 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.500 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.499 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.498 | |
| 5xra | FMN | Cannabinoid receptor 1 | / | 0.497 | |
| 2fcr | FMN | Flavodoxin | / | 0.494 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.494 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.493 | |
| 1xyy | FMN | Flavodoxin | / | 0.491 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.488 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.488 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.485 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.483 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.483 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.480 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.478 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.477 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.476 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.476 | |
| 1g6o | ADP | Cag alpha | / | 0.475 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.475 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.473 | |
| 3n3a | FMN | Protein NrdI | / | 0.473 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.471 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.470 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.469 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 4oxx | FMN | Cindoxin | / | 0.468 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.467 | |
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 0.467 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.467 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.466 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.465 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.464 | |
| 1czn | FMN | Flavodoxin | / | 0.464 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.464 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.463 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.463 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.463 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.462 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.462 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.461 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.461 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.461 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.461 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.461 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.460 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.459 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.459 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.458 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.458 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.458 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.456 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.456 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.456 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 4e2y | JHZ | Methyltransferase | / | 0.455 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.454 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.454 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.453 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.453 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.453 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.453 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.453 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.453 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 3kxo | KXO | Hematopoietic prostaglandin D synthase | / | 0.452 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.452 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.452 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.452 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.451 | |
| 3hr4 | FMN | Nitric oxide synthase, inducible | 1.14.13.39 | 0.451 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.451 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.450 | |
| 1t57 | FMN | Conserved protein | / | 0.450 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.450 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.450 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.450 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.449 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4pab | THG | Dimethylglycine dehydrogenase, mitochondrial | 1.5.8.4 | 0.449 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.448 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.448 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.448 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.448 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.448 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.447 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.447 | |
| 2vt4 | P32 | Beta-1 adrenergic receptor | / | 0.447 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.447 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.447 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.447 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.447 | |
| 5dp2 | NAP | CurF | / | 0.447 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.446 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 2v5u | FMN | Flavodoxin | / | 0.446 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.446 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.445 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.445 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.445 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.445 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.445 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1sg0 | STL | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.444 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.444 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3krf | IPE | Geranyl diphosphate synthase large subunit | / | 0.444 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3lv1 | NAP | NAD(P)-dependent benzaldehyde dehydrogenase | 1.2.1.28 | 0.443 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.443 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.443 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.442 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.442 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.442 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.442 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.442 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.441 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.441 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.441 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.441 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.441 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.440 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.440 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.440 | |
| 2ohi | FMN | Type A flavoprotein FprA | 1 | 0.440 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.440 |