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 |
|---|---|---|---|
| 1n43 | BTN | Streptavidin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1n43 | BTN | Streptavidin | / | 1.000 | |
| 1ndj | BTN | Streptavidin | / | 0.710 | |
| 1mep | BTN | Streptavidin | / | 0.640 | |
| 1n9m | BTN | Streptavidin | / | 0.619 | |
| 2zsc | BTN | Tamavidin2 | / | 0.607 | |
| 4bx7 | B4F | Streptavidin | / | 0.592 | |
| 1nqm | BTN | Streptavidin | / | 0.584 | |
| 1nc9 | IMI | Streptavidin | / | 0.583 | |
| 1swp | BTN | Streptavidin | / | 0.581 | |
| 1swp | BTQ | Streptavidin | / | 0.574 | |
| 3ry2 | BTN | Streptavidin | / | 0.574 | |
| 2rtq | IMI | Streptavidin | / | 0.571 | |
| 1swe | BTN | Streptavidin | / | 0.570 | |
| 1swd | BTN | Streptavidin | / | 0.564 | |
| 1swn | BTN | Streptavidin | / | 0.561 | |
| 2izg | BTN | Streptavidin | / | 0.561 | |
| 1lcw | SHM | Streptavidin | / | 0.560 | |
| 1stp | BTN | Streptavidin | / | 0.560 | |
| 2izh | BTN | Streptavidin | / | 0.559 | |
| 4dne | DTB | Streptavidin | / | 0.559 | |
| 4gd9 | BTN | Streptavidin | / | 0.559 | |
| 4bj8 | BTN | Avidin | / | 0.555 | |
| 1sre | HAB | Streptavidin | / | 0.554 | |
| 2rtg | BTN | Streptavidin | / | 0.554 | |
| 1mk5 | BTN | Streptavidin | / | 0.553 | |
| 4ggz | BTN | Bll1558 protein | / | 0.553 | |
| 2rtp | IMI | Streptavidin | / | 0.550 | |
| 1srg | MHB | Streptavidin | / | 0.548 | |
| 2izf | BTN | Streptavidin | / | 0.546 | |
| 2rtr | IMI | Streptavidin | / | 0.546 | |
| 4yvb | BTN | Streptavidin | / | 0.546 | |
| 1swt | BTN | Streptavidin | / | 0.545 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.543 | |
| 3wyp | BSO | Streptavidin | / | 0.543 | |
| 3vgw | NVZ | Avidin | / | 0.540 | |
| 1sri | DMB | Streptavidin | / | 0.538 | |
| 2rtd | BTN | Streptavidin | / | 0.537 | |
| 2rtf | BTN | Streptavidin | / | 0.537 | |
| 2y3f | BTN | Streptavidin | / | 0.534 | |
| 3vhh | VHH | Avidin | / | 0.531 | |
| 4gda | BTN | Streptavidin | / | 0.531 | |
| 1srf | MTB | Streptavidin | / | 0.529 | |
| 2izl | IMI | Streptavidin | / | 0.529 | |
| 3vhi | VHI | Avidin | / | 0.529 | |
| 1srh | MOB | Streptavidin | / | 0.527 | |
| 2jgs | BTN | Avidin | / | 0.525 | |
| 2rtn | IMI | Streptavidin | / | 0.525 | |
| 1i9h | BNI | Streptavidin | / | 0.524 | |
| 2rto | IMI | Streptavidin | / | 0.522 | |
| 1srj | NAB | Streptavidin | / | 0.515 | |
| 2rte | BTN | Streptavidin | / | 0.513 | |
| 3wzn | BTN | Streptavidin | / | 0.512 | |
| 1df8 | BTN | Streptavidin | / | 0.511 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.510 | |
| 3rdq | DTB | Streptavidin | / | 0.509 | |
| 1rxh | BNI | Streptavidin | / | 0.507 | |
| 1avd | BTN | Avidin | / | 0.506 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.504 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.501 | |
| 1swr | BTN | Streptavidin | / | 0.500 | |
| 2c4i | BTN | Avidin | / | 0.499 | |
| 1lcz | BH7 | Streptavidin | / | 0.498 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.495 | |
| 2rtm | IMI | Streptavidin | / | 0.495 | |
| 3wyq | BTN | Streptavidin | / | 0.495 | |
| 3vhm | NPK | Avidin | / | 0.493 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.491 | |
| 4z28 | BTN | Hoefavidin | / | 0.491 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.490 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.490 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.489 | |
| 2uz2 | BTN | Avd protein | / | 0.488 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.484 | |
| 1luq | BTN | Streptavidin | / | 0.481 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.480 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 3t2w | BTN | Avidin/streptavidin | / | 0.479 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.478 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.477 | |
| 2izj | BTN | Streptavidin | / | 0.475 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.474 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.473 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.473 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.473 | |
| 4bui | W2E | Tankyrase-2 | 2.4.2.30 | 0.472 | |
| 2avi | BTN | Avidin | / | 0.471 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.471 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.469 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.467 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.464 | |
| 2rti | GLL | Streptavidin | / | 0.464 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.463 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.462 | |
| 2izi | BTN | Streptavidin | / | 0.462 | |
| 4l09 | 1UR | Tankyrase-2 | 2.4.2.30 | 0.462 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.461 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2uyw | BTN | Avd protein | / | 0.460 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.460 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.460 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.458 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.458 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.456 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.456 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.455 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.455 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.455 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.455 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3ehj | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.454 | |
| 3f90 | FMN | Flavodoxin | / | 0.454 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.454 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4e32 | DWN | Methyltransferase | / | 0.453 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.453 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.452 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 2yhu | WHF | Pteridine reductase | / | 0.452 | |
| 4buf | F36 | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 5epo | TUD | 7-alpha-hydroxysteroid deydrogenase | / | 0.452 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1zdw | FLV | Prenyltransferase | / | 0.451 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.451 | |
| 3klb | FMN | Uncharacterized protein | / | 0.451 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.451 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.450 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.450 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 4bue | JQF | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.450 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3o8g | O8G | HTH-type transcriptional regulator EthR | / | 0.449 | |
| 4j3m | AJ8 | Tankyrase-2 | 2.4.2.30 | 0.449 | |
| 4n4w | SNT | Smoothened homolog | / | 0.449 | |
| 1fx1 | FMN | Flavodoxin | / | 0.448 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 3tp0 | FO5 | HTH-type transcriptional regulator EthR | / | 0.448 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4l34 | 1VG | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.447 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.447 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2eeq | SAH | Diphthine synthase | / | 0.446 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.446 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.445 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.445 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 4phl | PIL | Phosphodiesterase | / | 0.445 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.445 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.444 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.444 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.444 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.443 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.443 | |
| 1ycg | FMN | Nitric oxide reductase | 1 | 0.442 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 2izk | GLL | Streptavidin | / | 0.442 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.442 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3ebi | BEY | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3irh | DTP | HD domain protein | / | 0.442 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.442 | |
| 3l7g | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.442 | |
| 3wag | TYD | Glycosyltransferase | / | 0.442 | |
| 4hlf | 15Z | Tankyrase-2 | 2.4.2.30 | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.441 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.441 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.441 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.441 | |
| 3ndj | JHZ | Methyltransferase | / | 0.441 | |
| 3o8h | O8H | HTH-type transcriptional regulator EthR | / | 0.441 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.441 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.441 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.441 | |
| 4iei | ADP | Gene 2 protein | / | 0.441 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1c7o | PPG | Hemolysin | / | 0.440 | |
| 1eyy | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.440 | |
| 1i75 | NOJ | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.440 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 0.440 | |
| 3kr8 | XAV | Tankyrase-2 | 2.4.2.30 | 0.440 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 4kxj | P34 | Nucleoprotein | / | 0.440 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.440 |