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 |
|---|---|---|---|
| 2c4i | BTN | Avidin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2c4i | BTN | Avidin | / | 1.000 | |
| 1avd | BTN | Avidin | / | 0.585 | |
| 2avi | BTN | Avidin | / | 0.575 | |
| 2rtg | BTN | Streptavidin | / | 0.575 | |
| 2uyw | BTN | Avd protein | / | 0.575 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.552 | |
| 1rxh | BNI | Streptavidin | / | 0.548 | |
| 2izh | BTN | Streptavidin | / | 0.548 | |
| 2rtd | BTN | Streptavidin | / | 0.547 | |
| 2rtf | BTN | Streptavidin | / | 0.547 | |
| 2izl | IMI | Streptavidin | / | 0.546 | |
| 3ry2 | BTN | Streptavidin | / | 0.546 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.544 | |
| 2izg | BTN | Streptavidin | / | 0.540 | |
| 4dne | DTB | Streptavidin | / | 0.539 | |
| 2uz2 | BTN | Avd protein | / | 0.535 | |
| 2rte | BTN | Streptavidin | / | 0.534 | |
| 4gda | BTN | Streptavidin | / | 0.528 | |
| 1swt | BTN | Streptavidin | / | 0.527 | |
| 2rto | IMI | Streptavidin | / | 0.521 | |
| 2rtq | IMI | Streptavidin | / | 0.516 | |
| 1stp | BTN | Streptavidin | / | 0.515 | |
| 2izf | BTN | Streptavidin | / | 0.513 | |
| 3wzn | BTN | Streptavidin | / | 0.513 | |
| 2rtn | IMI | Streptavidin | / | 0.512 | |
| 4bx7 | B4F | Streptavidin | / | 0.511 | |
| 1mk5 | BTN | Streptavidin | / | 0.507 | |
| 2rti | GLL | Streptavidin | / | 0.507 | |
| 2izj | BTN | Streptavidin | / | 0.505 | |
| 2y3f | BTN | Streptavidin | / | 0.502 | |
| 1lcz | BH7 | Streptavidin | / | 0.500 | |
| 1sre | HAB | Streptavidin | / | 0.495 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.494 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.493 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.491 | |
| 3wyq | BTN | Streptavidin | / | 0.489 | |
| 1df8 | BTN | Streptavidin | / | 0.488 | |
| 1swr | BTN | Streptavidin | / | 0.487 | |
| 1luq | BTN | Streptavidin | / | 0.486 | |
| 1lcw | SHM | Streptavidin | / | 0.485 | |
| 1nqm | BTN | Streptavidin | / | 0.484 | |
| 1srg | MHB | Streptavidin | / | 0.484 | |
| 2izk | GLL | Streptavidin | / | 0.481 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.477 | |
| 1zdw | FLV | Prenyltransferase | / | 0.475 | |
| 2rtp | IMI | Streptavidin | / | 0.475 | |
| 2rtr | IMI | Streptavidin | / | 0.475 | |
| 1i9h | BNI | Streptavidin | / | 0.473 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.473 | |
| 1srh | MOB | Streptavidin | / | 0.473 | |
| 4bj8 | BTN | Avidin | / | 0.473 | |
| 2rtm | IMI | Streptavidin | / | 0.472 | |
| 2rtk | GLL | Streptavidin | / | 0.471 | |
| 4z28 | BTN | Hoefavidin | / | 0.471 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 4bqu | CLR | Japanin | / | 0.468 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.465 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.463 | |
| 2zsc | BTN | Tamavidin2 | / | 0.463 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1sri | DMB | Streptavidin | / | 0.461 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2izi | BTN | Streptavidin | / | 0.460 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 1srf | MTB | Streptavidin | / | 0.459 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.459 | |
| 1eio | GCH | Gastrotropin | / | 0.458 | |
| 1swn | BTN | Streptavidin | / | 0.458 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.458 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.457 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.457 | |
| 3ew2 | BTN | Hypothetical conserved protein | / | 0.457 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 1srj | NAB | Streptavidin | / | 0.455 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.455 | |
| 4yvb | BTN | Streptavidin | / | 0.455 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.454 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.453 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.453 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.453 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1nc9 | IMI | Streptavidin | / | 0.451 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.451 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1swe | BTN | Streptavidin | / | 0.450 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 2fvl | NAP | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | 0.449 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.448 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.448 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.446 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3t2w | BTN | Avidin/streptavidin | / | 0.445 | |
| 1swp | BTN | Streptavidin | / | 0.444 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1m9t | INE | Nitric oxide synthase, inducible | 1.14.13.39 | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3rdq | DTB | Streptavidin | / | 0.442 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.442 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.441 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.441 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.441 | |
| 1ef9 | 2CP | Methylmalonyl-CoA decarboxylase | 4.1.1.41 | 0.440 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.440 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.440 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.440 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.440 | |
| 4o7u | THF | Thymidylate synthase | / | 0.440 |