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 |
|---|---|---|---|
| 4fps | 0UX | Queuine tRNA-ribosyltransferase | 2.4.2.29 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4fps | 0UX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 1.000 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.791 | |
| 4gkt | 0O1 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.744 | |
| 4gh1 | 0WX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.716 | |
| 3sm0 | AEK | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.682 | |
| 4gh3 | 0EV | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.678 | |
| 4gg9 | 0WW | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.660 | |
| 3ge7 | AFQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.648 | |
| 1y5w | NEZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.636 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.625 | |
| 1q63 | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.622 | |
| 1q4w | DQU | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.614 | |
| 2z1x | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.601 | |
| 1y5x | E89 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.599 | |
| 4fsa | 0V3 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.594 | |
| 4gcx | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.594 | |
| 4fr1 | 0V2 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.593 | |
| 2bbf | 344 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.578 | |
| 2qzr | S79 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.578 | |
| 4giy | 0WY | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.577 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.575 | |
| 4hqv | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.572 | |
| 4q8p | CKR | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.571 | |
| 1y5v | NE8 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.564 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.559 | |
| 4hsh | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.559 | |
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.555 | |
| 1f3e | DPZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.550 | |
| 1efz | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.545 | |
| 4hvx | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.545 | |
| 1it7 | GUN | tRNA-guanine(15) transglycosylase | 2.4.2.48 | 0.544 | |
| 1q65 | BHB | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.541 | |
| 2pot | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.525 | |
| 3gc5 | 2MQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.520 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.514 | |
| 1r5y | DQU | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.513 | |
| 4h7z | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.511 | |
| 1n2v | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.506 | |
| 3bll | BPQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.500 | |
| 1q66 | KMB | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.493 | |
| 3ele | PLP | Aminotransferase | / | 0.488 | |
| 1pxg | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.476 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.475 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.470 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.470 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.468 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.467 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.467 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.467 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.464 | |
| 4e70 | N7I | Coniferyl alcohol 9-O-methyltransferase | / | 0.464 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2eer | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.463 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.462 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.462 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.462 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.461 | |
| 5a65 | TPP | Thiamine-triphosphatase | 3.6.1.28 | 0.461 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.459 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.459 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 1t1s | CBQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.458 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.458 | |
| 1efa | NPF | Lactose operon repressor | / | 0.457 | |
| 1vft | DCS | Alanine racemase | / | 0.457 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.457 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.456 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.456 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.456 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.455 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.455 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.454 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.454 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.453 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.453 | |
| 4js9 | H4B | Nitric oxide synthase, inducible | 1.14.13.39 | 0.453 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.452 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.452 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.452 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 2pid | YSA | Tyrosine--tRNA ligase, mitochondrial | 6.1.1.1 | 0.451 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4qjc | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1ivs | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.450 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 1uze | EAL | Angiotensin-converting enzyme | 3.2.1 | 0.450 | |
| 3aw9 | GDU | NAD-dependent epimerase/dehydratase | / | 0.450 | |
| 4ug5 | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.450 | |
| 1qw5 | H4B | Nitric oxide synthase, inducible | 1.14.13.39 | 0.449 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.449 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.449 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 4fex | 0TO | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.449 | |
| 1sm2 | STU | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.448 | |
| 3e6e | DCS | Alanine racemase | / | 0.448 | |
| 3p9t | TCL | Repressor | / | 0.448 | |
| 3qtt | ANP | Pantothenate synthetase | / | 0.448 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.448 | |
| 4lwa | Q13 | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.448 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.448 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.447 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4ug9 | 1EW | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.447 | |
| 3s6a | ANP | Adenosine monophosphate-protein transferase NmFic | 2.7.7.n1 | 0.446 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.446 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.445 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3nxt | D2E | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.444 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.444 | |
| 1ne6 | SP1 | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.443 | |
| 1ngb | ADP | Heat shock cognate 71 kDa protein | / | 0.443 | |
| 2y01 | Y00 | Beta-1 adrenergic receptor | / | 0.443 | |
| 3arv | SAU | Chitinase A | / | 0.443 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 3roe | THM | NAD(P)H-hydrate epimerase | 5.1.99.6 | 0.443 | |
| 4bwa | N0B | Pyrrolysine--tRNA ligase | / | 0.443 | |
| 4fvz | 4KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.443 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.442 | |
| 3c1x | CKK | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.442 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.441 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.441 | |
| 4c36 | ZO9 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.441 | |
| 4ug7 | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.441 | |
| 4uga | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.441 | |
| 2ycy | P32 | Beta-1 adrenergic receptor | / | 0.441 | |
| 1l0c | COT | Serotonin N-acetyltransferase | / | 0.440 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.440 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4buf | F36 | Tankyrase-2 | 2.4.2.30 | 0.440 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.440 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.440 |