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 |
|---|---|---|---|
| 3lzz | GDP | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3lzz | GDP | Uncharacterized protein | / | 1.000 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.496 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.489 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.488 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.485 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.485 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.483 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.482 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.482 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 1c7o | PPG | Hemolysin | / | 0.480 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.480 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.479 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.479 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.477 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.473 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.471 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.471 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.470 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.470 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.469 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.466 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.463 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.463 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.461 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4c2p | X8Z | Angiotensin-converting enzyme | 3.2.1 | 0.461 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 1qv0 | CZH | Obelin | / | 0.460 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.460 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.458 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.458 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.457 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.457 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.457 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.455 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.455 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 1el4 | CTZ | Obelin | / | 0.454 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.453 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.452 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.451 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.450 | |
| 3nfr | EWQ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.450 | |
| 1uhj | CZB | Aequorin-2 | / | 0.449 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.449 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.449 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2xy9 | 3ES | Angiotensin-converting enzyme | 3.2.1 | 0.449 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3dd0 | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.448 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.448 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.448 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.447 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.446 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.446 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.446 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.446 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.445 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1xr2 | C2F | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | 2.1.1.14 | 0.444 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.444 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.444 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.444 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.444 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.443 | |
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.443 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1s36 | CEI | Obelin | / | 0.442 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.442 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.442 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4nqg | CZH | Mitrocomin | / | 0.442 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1qv1 | CZH | Obelin | / | 0.441 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.441 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.441 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.441 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3r7m | SUZ | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.440 |