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 |
|---|---|---|---|
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 1.000 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 1.000 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.547 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.547 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.536 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.536 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.513 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.504 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.504 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.499 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.495 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.493 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.492 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.490 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.490 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.484 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.483 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.482 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.482 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.481 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.480 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.480 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.479 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.479 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.478 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.477 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.475 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.475 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.475 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.473 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.473 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.473 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.472 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.472 | |
| 1qrs | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.471 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.471 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.470 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.470 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.470 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.470 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.469 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.469 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.469 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.469 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.468 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.468 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.466 | |
| 4gqe | 6KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.465 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.464 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.464 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.463 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.462 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.462 | |
| 4ira | FAD | 4-hydroxyphenylacetate 3-monooxygenase | / | 0.461 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.460 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.460 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 4hh4 | SAH | CcbJ | / | 0.460 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.459 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.459 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.459 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.457 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.457 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.457 | |
| 3i0o | SMI | Spectinomycin phosphotransferase | / | 0.457 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.457 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.456 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.455 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.455 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.454 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.454 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.454 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.454 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.454 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.454 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.454 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.453 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.453 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.453 | |
| 5ilw | URI | Ribosome inactivating protein | / | 0.453 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.452 | |
| 2vjm | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.452 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.452 | |
| 4lay | I63 | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.452 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.451 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.451 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.451 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.451 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.450 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.450 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.450 | |
| 4dh0 | MR8 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.450 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.449 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.449 | |
| 3eku | CY9 | Actin-5C | / | 0.449 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.448 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.448 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.448 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.448 | |
| 2xb9 | XNW | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.448 | |
| 1bl4 | AP1 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 1gvr | TNL | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.447 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.447 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.447 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.447 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.447 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.447 | |
| 4fvz | 4KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.447 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.447 | |
| 4ami | G90 | Beta-1 adrenergic receptor | / | 0.447 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.446 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.446 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.446 | |
| 3dqr | JI2 | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.446 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.446 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.445 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 2x91 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.445 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.445 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 1acj | THA | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.444 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.444 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.444 | |
| 4fw0 | 5KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.444 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.444 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.443 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.443 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.443 | |
| 1fkh | SBX | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1qrt | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.442 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.442 | |
| 2vt4 | P32 | Beta-1 adrenergic receptor | / | 0.442 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.442 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.441 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.441 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.441 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.440 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.440 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.440 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.440 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.440 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.440 |