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 |
|---|---|---|---|
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 | / | 1.000 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.559 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.551 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.488 | |
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 0.481 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.481 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.477 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.475 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.474 | |
| 4e2x | TYD | Methyltransferase | / | 0.474 | |
| 4l4x | NDP | AmphI | / | 0.474 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.473 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.472 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.471 | |
| 1fue | FMN | Flavodoxin | / | 0.469 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.469 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.467 | |
| 1p4a | PCP | Pur operon repressor | / | 0.466 | |
| 2ewv | ADP | Twitching motility protein PilT | / | 0.466 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.464 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.464 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.463 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.463 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.463 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.462 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.461 | |
| 1zxn | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.460 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2hp2 | KE4 | Glutamate-1-semialdehyde 2,1-aminomutase | 5.4.3.8 | 0.460 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.459 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.459 | |
| 1ksz | PGS | Adenylosuccinate synthetase | / | 0.458 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.458 | |
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.458 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.457 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.457 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.457 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.456 | |
| 2prb | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.456 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.456 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.455 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.455 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.455 | |
| 4fiz | CUE | 17beta-hydroxysteroid dehydrogenase | / | 0.455 | |
| 4ikz | AFS | Di-tripeptide ABC transporter (Permease) | / | 0.455 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.454 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.454 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.454 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.454 | |
| 1akr | FMN | Flavodoxin | / | 0.453 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.453 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.453 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.453 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.453 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.453 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.453 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.453 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.452 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.452 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.452 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.452 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.452 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.452 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.452 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.452 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.452 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.452 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.451 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.451 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.451 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.451 | |
| 5hvn | NAD | 3-dehydroquinate synthase | / | 0.451 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.450 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.450 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.450 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.449 | |
| 2qtc | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.449 | |
| 4dc3 | 2FA | Putative adenosine kinase | / | 0.449 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 3eku | CY9 | Actin-5C | / | 0.448 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.448 | |
| 3zhz | FM7 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.448 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.447 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.447 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.447 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.446 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.446 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.446 | |
| 5f8u | P32 | Beta-1 adrenergic receptor | / | 0.446 | |
| 1c7f | FMN | Flavodoxin | / | 0.445 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 1qy5 | NEC | Endoplasmin | / | 0.445 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.445 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.445 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.445 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.445 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.444 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 2ejz | SAH | Diphthine synthase | / | 0.444 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.444 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.444 | |
| 3ogx | H1S | Peptidoglycan recognition protein 1 | / | 0.444 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.444 | |
| 4e2z | JHZ | Methyltransferase | / | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4hh4 | SAH | CcbJ | / | 0.444 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.444 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.443 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.443 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.443 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.443 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.443 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.443 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.442 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.442 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.442 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 1fwy | UD1 | Bifunctional protein GlmU | / | 0.441 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.441 | |
| 2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.441 | |
| 4e32 | DWN | Methyltransferase | / | 0.441 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1cg0 | IMO | Adenylosuccinate synthetase | / | 0.440 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.440 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1g5q | ASP_SER_TYR_THR_CYS | Epidermin decarboxylase | 4.1.1 | 0.440 | |
| 1l2o | ADP | Myosin heavy chain, striated muscle | / | 0.440 | |
| 1n2j | PAF | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 1ofv | FMN | Flavodoxin | / | 0.440 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.440 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.440 | |
| 2ft0 | ACO | dTDP-fucosamine acetyltransferase | / | 0.440 | |
| 2r8p | T6F | Transketolase 1 | / | 0.440 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.440 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.440 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.440 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.440 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.440 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.440 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.440 |