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 |
|---|---|---|---|
| 4ikr | PVP | Methionine aminopeptidase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 1.000 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.794 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.768 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.686 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.634 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.633 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.632 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.615 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.601 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.601 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.594 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.592 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.591 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.578 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.575 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.573 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.569 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.567 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.561 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.557 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.555 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.555 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.548 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.547 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.538 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.533 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.532 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.529 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.523 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.518 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.515 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.509 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.508 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.504 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.500 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.498 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.489 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.488 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.482 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.482 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.475 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.475 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.475 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.473 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.472 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.470 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.467 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.466 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.461 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 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 | 0.459 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.458 | |
| 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 | 0.457 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 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 | 0.452 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.451 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.449 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.447 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.446 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.446 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.445 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.445 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.444 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.444 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.443 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.443 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.442 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.442 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.442 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.442 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.442 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.442 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.441 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 1jf0 | CZH | Obelin | / | 0.440 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.440 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.440 |