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 |
|---|---|---|---|
| 4wa7 | GDP | GTPase KRas |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4wa7 | GDP | GTPase KRas | / | 1.000 | |
| 4l9s | GDP | GTPase HRas | / | 0.672 | |
| 4lpk | GDP | GTPase KRas | / | 0.636 | |
| 4epw | GDP | GTPase KRas | / | 0.633 | |
| 4l8g | GDP | GTPase KRas | / | 0.625 | |
| 4tq9 | GDP | GTPase KRas | / | 0.620 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.615 | |
| 4lv6 | GDP | GTPase KRas | / | 0.609 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.607 | |
| 2rgg | GNP | GTPase HRas | / | 0.605 | |
| 3k9l | GNP | GTPase HRas | / | 0.604 | |
| 2ce2 | GDP | GTPase HRas | / | 0.601 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.600 | |
| 3tgp | GNP | GTPase HRas | / | 0.598 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.598 | |
| 4q02 | GDP | GTPase KRas | / | 0.595 | |
| 4q03 | GDP | GTPase KRas | / | 0.595 | |
| 4ql3 | GDP | GTPase KRas | / | 0.593 | |
| 4xvq | GNP | GTPase HRas | / | 0.593 | |
| 2rge | GNP | GTPase HRas | / | 0.587 | |
| 4obe | GDP | GTPase KRas | / | 0.587 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.577 | |
| 1lfd | GNP | GTPase HRas | / | 0.575 | |
| 4ldj | GDP | GTPase KRas | / | 0.575 | |
| 3oiu | GNP | GTPase HRas | / | 0.574 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.573 | |
| 3lbh | GNP | GTPase HRas | / | 0.569 | |
| 3oiw | GNP | GTPase HRas | / | 0.567 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.566 | |
| 3ddc | GNP | GTPase HRas | / | 0.565 | |
| 4dsn | GCP | GTPase KRas | / | 0.564 | |
| 4nyj | GNP | GTPase HRas | / | 0.564 | |
| 4lrw | GDP | GTPase KRas | / | 0.563 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.563 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.562 | |
| 4epx | GDP | GTPase KRas | / | 0.562 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.559 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.559 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.558 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.557 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.556 | |
| 4nyi | GNP | GTPase HRas | / | 0.556 | |
| 3i3s | GNP | GTPase HRas | / | 0.554 | |
| 2rgc | GNP | GTPase HRas | / | 0.551 | |
| 4xvr | GNP | GTPase HRas | / | 0.551 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.549 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.548 | |
| 4g0n | GNP | GTPase HRas | / | 0.548 | |
| 4dlw | GNP | GTPase HRas | / | 0.547 | |
| 3oiv | GNP | GTPase HRas | / | 0.546 | |
| 3v4f | GNP | GTPase HRas | / | 0.546 | |
| 2rgb | GNP | GTPase HRas | / | 0.545 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.544 | |
| 3lbi | GNP | GTPase HRas | / | 0.543 | |
| 3rs4 | GNP | GTPase HRas | / | 0.543 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.543 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.539 | |
| 2c5l | GTP | GTPase HRas | / | 0.538 | |
| 5b2z | GNP | GTPase HRas | / | 0.538 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.537 | |
| 3rs5 | GNP | GTPase HRas | / | 0.535 | |
| 2cl6 | CAG | GTPase HRas | / | 0.534 | |
| 3l8y | GNP | GTPase HRas | / | 0.532 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.531 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.531 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.530 | |
| 4dlx | GNP | GTPase HRas | / | 0.530 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.529 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.529 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.528 | |
| 3k8y | GNP | GTPase HRas | / | 0.528 | |
| 3lbn | GNP | GTPase HRas | / | 0.526 | |
| 3rs0 | GNP | GTPase HRas | / | 0.526 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.523 | |
| 4dlv | GNP | GTPase HRas | / | 0.522 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.520 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.519 | |
| 4dlz | GNP | GTPase HRas | / | 0.519 | |
| 4dsu | GDP | GTPase KRas | / | 0.519 | |
| 4dlt | GNP | GTPase HRas | / | 0.518 | |
| 3kud | GDP | GTPase HRas | / | 0.517 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.516 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.515 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.515 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.513 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.512 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.510 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.510 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.510 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.510 | |
| 3rsl | GNP | GTPase HRas | / | 0.509 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.507 | |
| 4dls | GNP | GTPase HRas | / | 0.506 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.504 | |
| 3rs7 | GNP | GTPase HRas | / | 0.502 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.501 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.500 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.500 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.499 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.498 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.497 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.496 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.496 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.494 | |
| 4dso | GSP | GTPase KRas | / | 0.494 | |
| 4l9w | GNP | GTPase HRas | / | 0.494 | |
| 4mit | GTP | Rho-related protein racC | / | 0.493 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.492 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.491 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.491 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.490 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.488 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.488 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 2mse | GNP | MHC class I alpha chain | / | 0.487 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.486 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.486 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 3ref | GDP | Rho family GTPase | / | 0.485 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.485 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.482 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.482 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.482 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.480 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.479 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.477 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.477 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.477 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.474 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.473 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.472 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.472 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.470 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.469 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.469 | |
| 1ii6 | ADP | Kinesin-like protein KIF11 | / | 0.468 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.468 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.467 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.465 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.465 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.464 | |
| 1jdv | ADN | Purine nucleoside phosphorylase | / | 0.464 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.463 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.463 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.462 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.462 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.462 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.461 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.460 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.460 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.459 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.458 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.457 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.455 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 2bxm | IMN | Serum albumin | / | 0.455 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.455 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.453 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.452 | |
| 4jdc | NAD | Probable pyrroline-5-carboxylate dehydrogenase RocA | / | 0.452 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.452 | |
| 3cob | ADP | Kinesin heavy chain-like protein | / | 0.451 | |
| 3sbe | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.451 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.451 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.450 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 3moh | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.450 | |
| 1o01 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.448 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.448 | |
| 2ati | IHU | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.448 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.448 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.447 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.447 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.447 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.447 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1mzc | BNE | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.446 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.446 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.446 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.446 | |
| 1mbz | IOT | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.445 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.445 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.445 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1n2b | PAF | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 1r2j | FAD | FkbI | / | 0.444 | |
| 3x03 | ANP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.444 | |
| 4mvc | CDC | Choline-phosphate cytidylyltransferase A | / | 0.444 | |
| 5iot | UMP | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.444 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.443 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.443 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 2xvv | 9DN | Serum albumin | / | 0.443 | |
| 4iwy | ADP | Ribosomal protein S6--L-glutamate ligase | / | 0.443 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.442 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.442 | |
| 2xvw | 9NR | Serum albumin | / | 0.442 | |
| 3eku | CY9 | Actin-5C | / | 0.442 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.442 | |
| 4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.442 | |
| 4ku3 | MYA | 3-oxoacyl-[ACP] synthase III | / | 0.442 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.442 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.442 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.441 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.441 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3gwn | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.441 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.441 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.441 | |
| 5ify | TRH | Glucose-1-phosphate thymidylyltransferase | / | 0.441 | |
| 1jcq | 739 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.440 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2o2y | TCL | Enoyl-ACP reductase | / | 0.440 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3pft | FMN | Flavin reductase | / | 0.440 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.440 |