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 |
|---|---|---|---|
| 1srj | NAB | Streptavidin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1srj | NAB | Streptavidin | / | 1.000 | |
| 1sri | DMB | Streptavidin | / | 0.656 | |
| 1srh | MOB | Streptavidin | / | 0.630 | |
| 1srf | MTB | Streptavidin | / | 0.619 | |
| 1sre | HAB | Streptavidin | / | 0.617 | |
| 1srg | MHB | Streptavidin | / | 0.613 | |
| 2rtr | IMI | Streptavidin | / | 0.602 | |
| 1i9h | BNI | Streptavidin | / | 0.596 | |
| 4bx7 | B4F | Streptavidin | / | 0.593 | |
| 2rto | IMI | Streptavidin | / | 0.586 | |
| 1lcz | BH7 | Streptavidin | / | 0.583 | |
| 1swt | BTN | Streptavidin | / | 0.583 | |
| 2rtd | BTN | Streptavidin | / | 0.577 | |
| 2rte | BTN | Streptavidin | / | 0.567 | |
| 2rtg | BTN | Streptavidin | / | 0.567 | |
| 2izl | IMI | Streptavidin | / | 0.564 | |
| 1stp | BTN | Streptavidin | / | 0.562 | |
| 2rtp | IMI | Streptavidin | / | 0.561 | |
| 3wzn | BTN | Streptavidin | / | 0.561 | |
| 3rdq | DTB | Streptavidin | / | 0.560 | |
| 2rtf | BTN | Streptavidin | / | 0.557 | |
| 4gda | BTN | Streptavidin | / | 0.557 | |
| 2rti | GLL | Streptavidin | / | 0.556 | |
| 3ry2 | BTN | Streptavidin | / | 0.553 | |
| 2izh | BTN | Streptavidin | / | 0.552 | |
| 2rtq | IMI | Streptavidin | / | 0.544 | |
| 2izg | BTN | Streptavidin | / | 0.543 | |
| 1rxh | BNI | Streptavidin | / | 0.538 | |
| 4dne | DTB | Streptavidin | / | 0.536 | |
| 1lcw | SHM | Streptavidin | / | 0.528 | |
| 2y3f | BTN | Streptavidin | / | 0.528 | |
| 4z28 | BTN | Hoefavidin | / | 0.521 | |
| 2rtn | IMI | Streptavidin | / | 0.520 | |
| 1mk5 | BTN | Streptavidin | / | 0.519 | |
| 2izf | BTN | Streptavidin | / | 0.519 | |
| 2izk | GLL | Streptavidin | / | 0.518 | |
| 1luq | BTN | Streptavidin | / | 0.517 | |
| 2izi | BTN | Streptavidin | / | 0.517 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.515 | |
| 2rtm | IMI | Streptavidin | / | 0.511 | |
| 1df8 | BTN | Streptavidin | / | 0.510 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.510 | |
| 3wyq | BTN | Streptavidin | / | 0.506 | |
| 2uyw | BTN | Avd protein | / | 0.500 | |
| 1swn | BTN | Streptavidin | / | 0.497 | |
| 2rtk | GLL | Streptavidin | / | 0.496 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.493 | |
| 4gd9 | BTN | Streptavidin | / | 0.493 | |
| 2uz2 | BTN | Avd protein | / | 0.492 | |
| 1avd | BTN | Avidin | / | 0.487 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.487 | |
| 1swe | BTN | Streptavidin | / | 0.484 | |
| 2c4i | BTN | Avidin | / | 0.482 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.481 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.481 | |
| 1iiu | RTL | Retinol-binding protein 4 | / | 0.480 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 2avi | BTN | Avidin | / | 0.479 | |
| 2zsc | BTN | Tamavidin2 | / | 0.478 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.477 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.475 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.473 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 2a5c | 8DA | Avidin | / | 0.472 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.472 | |
| 3arq | DM5 | Chitinase A | / | 0.471 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.470 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.470 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.470 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2jgs | BTN | Avidin | / | 0.469 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.469 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.468 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.466 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.465 | |
| 2izj | BTN | Streptavidin | / | 0.465 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.465 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.461 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.459 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.459 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.459 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1mep | BTN | Streptavidin | / | 0.457 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.457 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.456 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.456 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 1ne6 | SP1 | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.455 | |
| 2fto | TMP | Thymidylate synthase | / | 0.455 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.455 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.454 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.454 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.454 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.453 | |
| 1hnd | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.453 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.453 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3ew2 | BTN | Hypothetical conserved protein | / | 0.453 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.453 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3t2w | BTN | Avidin/streptavidin | / | 0.452 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.452 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.451 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.451 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.450 | |
| 1nc9 | IMI | Streptavidin | / | 0.449 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.449 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.449 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.449 | |
| 3arv | SAU | Chitinase A | / | 0.449 | |
| 3pld | F90 | Endothiapepsin | 3.4.23.22 | 0.449 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.449 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.448 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.448 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.448 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.448 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.447 | |
| 1ndj | BTN | Streptavidin | / | 0.447 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.447 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.447 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.447 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.447 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.446 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1xp8 | AGS | Protein RecA | / | 0.446 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.446 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.446 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.446 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 2xtb | KRM | Adenosine kinase, putative | / | 0.446 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.446 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.446 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.446 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3up3 | XCA | aceDAF-12 | / | 0.446 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.446 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1e2n | RCA | Thymidine kinase | / | 0.445 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1r8q | AFB | Cytohesin-2 | / | 0.445 | |
| 1r8q | AFB | ADP-ribosylation factor 1 | / | 0.445 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.445 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.445 | |
| 1jtq | LY3 | Thymidylate synthase | / | 0.444 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.444 | |
| 1tys | DHF | Thymidylate synthase | / | 0.444 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.444 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.444 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4eil | CB3 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 4kxn | 6K6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.444 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.444 | |
| 1cgz | STL | Chalcone synthase 2 | 2.3.1.74 | 0.443 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.443 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.443 | |
| 3vgw | NVZ | Avidin | / | 0.443 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4dli | IRG | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 5fkk | TDC | Tetracycline repressor protein class D | / | 0.443 | |
| 5hbs | RTL | Retinol-binding protein 1 | / | 0.443 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.442 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1rxj | BNI | Streptavidin | / | 0.442 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.442 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.442 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4hl1 | ZZ7 | Metallo-beta-lactamase type 2 | / | 0.442 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.442 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.442 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.442 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.442 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.441 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.441 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.441 | |
| 1skg | VAL_ALA_PHE_ARG_SER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.441 | |
| 2g2h | P16 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.441 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3wyp | BSO | Streptavidin | / | 0.441 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.441 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.441 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.441 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.440 | |
| 1lqa | NDP | Protein tas | / | 0.440 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.440 | |
| 2f0y | 3MN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.440 |