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 |
|---|---|---|---|
| 4ea3 | 0NN | Nociceptin receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ea3 | 0NN | Nociceptin receptor | / | 1.000 | |
| 5dhg | DGV | Nociceptin receptor | / | 0.630 | |
| 5dhh | DGW | Nociceptin receptor | / | 0.594 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.493 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.489 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.482 | |
| 3nun | JMZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.480 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.479 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 4ej4 | EJ4 | Delta-type opioid receptor | / | 0.478 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.478 | |
| 2k62 | ITL | Fatty acid-binding protein, liver | / | 0.477 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.476 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.470 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 3qcq | 3Q0 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.467 | |
| 4dt9 | GMP | APH(2'')-Id | / | 0.467 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.467 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.466 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.466 | |
| 4jxr | ACO | Acetyltransferase | / | 0.466 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.465 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.465 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.465 | |
| 3cbl | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.464 | |
| 4u7w | NDP | MxaA | / | 0.464 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.463 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.461 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.461 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.461 | |
| 3bkb | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.461 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.461 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.460 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.460 | |
| 4yzc | STU | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.460 | |
| 4ekl | 0RF | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.459 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.458 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.457 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.457 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.457 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.457 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 3cr3 | ADP | PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.456 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.456 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.456 | |
| 3p2o | NAD | Bifunctional protein FolD | / | 0.456 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.456 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.455 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.455 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.455 | |
| 4bib | IEO | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.455 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.455 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.455 | |
| 1ao0 | 5GP | Amidophosphoribosyltransferase | / | 0.454 | |
| 3cd3 | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.454 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.454 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.453 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.453 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.453 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.453 | |
| 4tnb | SGV | G protein-coupled receptor kinase 5 | 2.7.11.16 | 0.453 | |
| 4u0o | MTA | Lipoyl synthase 2 | / | 0.453 | |
| 4yhj | AN2 | G protein-coupled receptor kinase 4 | 2.7.11.16 | 0.453 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.452 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3qcs | 3Q1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.451 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.451 | |
| 1mei | MOA | Inosine-5'-monophosphate dehydrogenase | / | 0.451 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3a62 | STU | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.451 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.451 | |
| 4ftt | 6HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.450 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4few | PP2 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.450 | |
| 4l44 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.450 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.450 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 3oe5 | 611 | Catechol O-methyltransferase | 2.1.1.6 | 0.449 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.449 | |
| 5auz | GEN | Death-associated protein kinase 1 | 2.7.11.1 | 0.449 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.448 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.448 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1uvr | BI8 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.448 | |
| 4ks8 | B49 | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.448 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.447 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.447 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.447 | |
| 4z87 | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.447 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.447 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 2acw | UPG | Glycosyltransferase | / | 0.446 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3lpb | NVB | Tyrosine-protein kinase JAK2 | / | 0.446 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.445 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.445 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.445 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.445 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.445 | |
| 4c8g | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.445 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.445 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.444 | |
| 3dhb | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.444 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.444 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.443 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.443 | |
| 2od7 | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.443 | |
| 2pvn | P63 | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.443 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.443 | |
| 4f3g | KAI | Glutamate receptor 3 | / | 0.443 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.443 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.443 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.442 | |
| 2pui | ADP | Methylthioribose kinase | 2.7.1.100 | 0.442 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.442 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.442 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 3nfr | EWQ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.442 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.441 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 1snu | STU | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.441 | |
| 2bxm | IMN | Serum albumin | / | 0.441 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.441 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.441 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.441 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.441 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.441 | |
| 4l43 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.441 | |
| 5ca0 | ACP | Tubulin tyrosine ligase | / | 0.441 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.441 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.441 | |
| 1q1w | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.440 | |
| 2cdu | FAD | NADH oxidase | / | 0.440 | |
| 2eb3 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.440 |