sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4fx2 | FMN | Flavodoxin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4fx2 | FMN | Flavodoxin | / | 1.000 | |
| 1fx1 | FMN | Flavodoxin | / | 0.722 | |
| 1j9g | FMN | Flavodoxin | / | 0.607 | |
| 1bu5 | RBF | Flavodoxin | / | 0.595 | |
| 5fx2 | FMN | Flavodoxin | / | 0.593 | |
| 1azl | FMN | Flavodoxin | / | 0.589 | |
| 3f6r | FMN | Flavodoxin | / | 0.585 | |
| 2fx2 | FMN | Flavodoxin | / | 0.580 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.571 | |
| 1aku | FMN | Flavodoxin | / | 0.561 | |
| 1wsb | FMN | Flavodoxin | / | 0.549 | |
| 1xyv | FMN | Flavodoxin | / | 0.543 | |
| 1j8q | FMN | Flavodoxin | / | 0.538 | |
| 1akr | FMN | Flavodoxin | / | 0.532 | |
| 1c7f | FMN | Flavodoxin | / | 0.526 | |
| 1akw | FMN | Flavodoxin | / | 0.522 | |
| 3kaq | FMN | Flavodoxin | / | 0.515 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.513 | |
| 3kap | FMN | Flavodoxin | / | 0.512 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.507 | |
| 5xr8 | FMN | Cannabinoid receptor 1 | / | 0.502 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.499 | |
| 5xra | FMN | Cannabinoid receptor 1 | / | 0.497 | |
| 2fcr | FMN | Flavodoxin | / | 0.494 | |
| 3f90 | FMN | Flavodoxin | / | 0.494 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.492 | |
| 1xyy | FMN | Flavodoxin | / | 0.489 | |
| 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 | 0.482 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.482 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.477 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.474 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.473 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.472 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.472 | |
| 3n3a | FMN | Protein NrdI | / | 0.471 | |
| 4oxx | FMN | Cindoxin | / | 0.468 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.467 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.467 | |
| 4k37 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.467 | |
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 0.466 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 1czn | FMN | Flavodoxin | / | 0.464 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.463 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.463 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.461 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.461 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.460 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.460 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.460 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.459 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.458 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.456 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.456 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.456 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.456 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.454 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.454 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.453 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.453 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.453 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.453 | |
| 3rim | TPP | Transketolase | 2.2.1.1 | 0.453 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.453 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.453 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.452 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.452 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.450 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.450 | |
| 4ckr | DI1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.450 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.450 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1t57 | FMN | Conserved protein | / | 0.449 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.448 | |
| 2bqz | SAH | N-lysine methyltransferase KMT5A | / | 0.448 | |
| 3gu3 | SAH | Methyltransferase | / | 0.448 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.448 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.448 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.448 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.447 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.447 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.447 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.447 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.447 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.447 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.447 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.446 | |
| 2vt4 | P32 | Beta-1 adrenergic receptor | / | 0.446 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.445 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2wzm | NA7 | Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346 | / | 0.445 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.445 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.445 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.445 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.445 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.444 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.443 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.443 | |
| 2r8p | T6F | Transketolase 1 | / | 0.443 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.443 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.442 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.442 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.441 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.441 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.441 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.441 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.441 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.441 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.440 | |
| 4e2y | JHZ | Methyltransferase | / | 0.440 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.440 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.440 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.440 |