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 |
|---|---|---|---|
| 1j8u | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1j8u | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 1.000 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.641 | |
| 5pah | LDP | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.610 | |
| 4pah | LNR | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.597 | |
| 1lrm | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.580 | |
| 1tg2 | H2B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.575 | |
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.548 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.501 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.498 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.493 | |
| 3up3 | XCA | aceDAF-12 | / | 0.480 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.479 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.474 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.473 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.472 | |
| 3vet | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.472 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.469 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.467 | |
| 4x5g | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.466 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.465 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.464 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.464 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.464 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.463 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.461 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.461 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1zw9 | H64 | ATP-dependent molecular chaperone HSP82 | / | 0.460 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.460 | |
| 1j3j | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.458 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.458 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.458 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.456 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.456 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.456 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.455 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.455 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.454 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.454 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.454 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.454 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.454 | |
| 1ndy | FR3 | Adenosine deaminase | 3.5.4.4 | 0.453 | |
| 1syn | F89 | Thymidylate synthase | / | 0.453 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.453 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3glu | LYS_VAL_MET | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.453 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.453 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.452 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.452 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.452 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1xqp | 8HG | N-glycosylase/DNA lyase | / | 0.449 | |
| 2cje | DUN | DUTPase | / | 0.449 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.449 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.449 | |
| 1rzy | 5AS | Histidine triad nucleotide-binding protein 1 | 3 | 0.448 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.447 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4phl | PIL | Phosphodiesterase | / | 0.447 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.446 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.446 | |
| 2vte | IK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.446 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.446 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.445 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.445 | |
| 2wug | HPK | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.445 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.445 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3up0 | D7S | aceDAF-12 | / | 0.445 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1bxs | NAD | Retinal dehydrogenase 1 | 1.2.1.36 | 0.444 | |
| 1jum | BER | HTH-type transcriptional regulator QacR | / | 0.444 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.444 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.444 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.444 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.444 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.444 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.444 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.443 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.443 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.443 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.443 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.443 | |
| 2zym | ACX | Periplasmic binding protein | / | 0.443 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.443 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.443 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.442 | |
| 1tdu | DUR | Thymidylate synthase | / | 0.442 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.442 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 2ejz | SAH | Diphthine synthase | / | 0.442 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.442 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.442 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.442 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.442 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.441 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4fh5 | UTP | Terminal uridylyltransferase cid1 | / | 0.441 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.441 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.441 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.440 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.440 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.440 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3vf2 | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.440 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.440 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.440 |