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 |
|---|---|---|---|
| 5ief | NBV | Neutral alpha-glucosidase AB | 3.2.1.84 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5ief | NBV | Neutral alpha-glucosidase AB | 3.2.1.84 | 1.000 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.528 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.517 | |
| 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 | 0.499 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.496 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 3lzz | GDP | Uncharacterized protein | / | 0.488 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.483 | |
| 2nm2 | NEU | Dihydroneopterin aldolase | / | 0.479 | |
| 2aov | C2M | Histamine N-methyltransferase | 2.1.1.8 | 0.478 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.478 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.477 | |
| 3ryk | TYD | dTDP-4-dehydrorhamnose 3,5-epimerase | / | 0.476 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.475 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.475 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.473 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.473 | |
| 1e1f | PSG | 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 | 0.472 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.472 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.471 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.471 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.471 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.469 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.469 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.468 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.467 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.466 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.464 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.464 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.463 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.463 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.463 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.463 | |
| 1el4 | CTZ | Obelin | / | 0.462 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.462 | |
| 1t41 | ID5 | Aldose reductase | 1.1.1.21 | 0.462 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.462 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.461 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.461 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3g5i | DNB | Pyrimidine-specific ribonucleoside hydrolase RihA | / | 0.460 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4n1f | CZH | Obelin | / | 0.460 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.459 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.459 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.458 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.457 | |
| 1s36 | CEI | Obelin | / | 0.457 | |
| 1us0 | LDT | Aldose reductase | 1.1.1.21 | 0.457 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3ptq | NFG | Beta-glucosidase 12 | / | 0.457 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.457 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.457 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.457 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.456 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.456 | |
| 4cb6 | 29R | Polymerase basic protein 2 | / | 0.456 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.456 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.456 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.455 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.455 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.455 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.454 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.454 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1r4l | XX5 | Angiotensin-converting enzyme 2 | 3.4.17.23 | 0.453 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.453 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.453 | |
| 4lrh | FOL | Folate receptor alpha | / | 0.453 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.452 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.452 | |
| 3rgz | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.452 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.451 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.451 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4mm4 | 8PR | Na(+):neurotransmitter symporter (Snf family) | / | 0.451 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.450 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.450 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.450 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.450 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3ghu | LDT | Aldose reductase | 1.1.1.21 | 0.450 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.450 | |
| 4bis | 8HQ | Lysine-specific demethylase 4A | 1.14.11 | 0.450 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.450 | |
| 4rxs | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.450 | |
| 4gd9 | BTN | Streptavidin | / | 0.449 | |
| 4nqg | CZH | Mitrocomin | / | 0.449 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.448 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3gx9 | TXD | Morphinone reductase | / | 0.448 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.448 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.448 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.447 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.447 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.446 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.446 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.445 | |
| 1g93 | UPG | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.445 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.445 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.445 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.444 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.444 | |
| 4gi5 | FAD | Putative NAD(P)H dehydrogenase (Quinone) | / | 0.444 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 5brp | PNG | Glycoside Hydrolase Family 13 | / | 0.444 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1qv0 | CZH | Obelin | / | 0.443 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.443 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.443 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.443 | |
| 4ts7 | ADP | Purine phosphoribosyltransferase (GpT-1) | / | 0.443 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.442 | |
| 1hv9 | UD1 | Bifunctional protein GlmU | / | 0.442 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.442 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.442 | |
| 2gmu | PDG | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.442 | |
| 2i17 | LDT | Aldose reductase | 1.1.1.21 | 0.442 | |
| 2iki | 388 | Aldose reductase | 1.1.1.21 | 0.442 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3d2d | REN | Reticuline oxidase | 1.21.3.3 | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.442 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3r8h | ZOM | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.442 | |
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.442 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.442 | |
| 1fkg | SB3 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1lc3 | NAD | Biliverdin reductase A | 1.3.1.24 | 0.441 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3ele | PLP | Aminotransferase | / | 0.441 | |
| 4olf | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.441 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.441 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.440 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 1t40 | ID5 | Aldose reductase | 1.1.1.21 | 0.440 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.440 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.440 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.440 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4kn2 | LYA | Folate receptor beta | / | 0.440 | |
| 4tny | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 | |
| 4to1 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 |