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 |
|---|---|---|---|
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 1.000 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.684 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.672 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.669 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.668 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.650 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.635 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.634 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.629 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.628 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.617 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.613 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.610 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.604 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.597 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.595 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.594 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.594 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.592 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.590 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.589 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.585 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.584 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.584 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.581 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.580 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.580 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.579 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.577 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.577 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.574 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.574 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.574 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.572 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.570 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.568 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.568 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.565 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.563 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.561 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.560 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.559 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.559 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.559 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.558 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.556 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.553 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.551 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.551 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.550 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.549 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.547 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.546 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.543 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.542 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.541 | |
| 3sl8 | JN7 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.538 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.537 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.535 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.534 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.531 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.531 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.531 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.530 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.529 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.527 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.524 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.521 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.521 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.520 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.519 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.512 | |
| 1rkp | IBM | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.511 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.511 | |
| 4phl | PIL | Phosphodiesterase | / | 0.510 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.504 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.503 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.502 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.501 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.492 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.491 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.490 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.489 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.488 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.486 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.484 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.475 | |
| 4myq | 19T | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.475 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.469 | |
| 1kuy | COT | Serotonin N-acetyltransferase | / | 0.468 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3up3 | XCA | aceDAF-12 | / | 0.464 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.461 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.461 | |
| 1c7o | PPG | Hemolysin | / | 0.459 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.459 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.458 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3f6s | FMN | Flavodoxin | / | 0.456 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.456 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 3n5w | XFJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.455 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.453 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.453 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.452 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.452 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.451 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.450 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.449 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.449 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.448 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.447 | |
| 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 | 0.447 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.447 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.447 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.447 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 3c1o | NAP | Eugenol synthase | / | 0.445 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.444 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.443 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 3w0t | HPU | Lactoylglutathione lyase | 4.4.1.5 | 0.443 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.442 | |
| 2zi6 | 3D1 | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.441 | |
| 3lnb | COA | N-acetyltransferase family protein | / | 0.441 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.441 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.441 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 2xej | OKD | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.440 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.440 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.440 |