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 |
|---|---|---|---|
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 1.000 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.653 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.647 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.643 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.635 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.626 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.626 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.625 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.623 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.621 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.619 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.612 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.612 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.610 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.609 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.608 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.608 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.607 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.606 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.605 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.604 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.603 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.602 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.602 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.601 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.600 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.599 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.599 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.597 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.596 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.595 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.594 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.592 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.590 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.588 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.588 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.588 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.588 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.584 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.583 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.579 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.578 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.578 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.577 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.577 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.576 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.575 | |
| 3sl8 | JN7 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.571 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.565 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.564 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.561 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.561 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.557 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.556 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.555 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.555 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.554 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.552 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.550 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.549 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.547 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.546 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.545 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.544 | |
| 4phl | PIL | Phosphodiesterase | / | 0.544 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.541 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.535 | |
| 4myq | 19T | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.534 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.532 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.532 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.531 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.527 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.519 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.519 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.519 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.519 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.517 | |
| 1rkp | IBM | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.516 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.514 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.513 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.512 | |
| 4htx | 19F | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.512 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.511 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.509 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.505 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.502 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.499 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.494 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.484 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.480 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.476 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3aba | FLI | Cytochrome P450 | / | 0.468 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.466 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.462 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.457 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.455 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.455 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.454 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2pl0 | STI | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.453 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 3be2 | RAJ | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.450 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.449 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.446 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.446 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.445 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.445 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.444 | |
| 3n5w | XFJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.441 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.441 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.440 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.440 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 |