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 |
|---|---|---|---|
| 1w2c | ANP | Inositol-trisphosphate 3-kinase A | 2.7.1.127 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1w2c | ANP | Inositol-trisphosphate 3-kinase A | 2.7.1.127 | 1.000 | |
| 1w2d | ADP | Inositol-trisphosphate 3-kinase A | 2.7.1.127 | 0.624 | |
| 4lv8 | ADP | Rhoptry protein 5 C | / | 0.489 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.488 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.485 | |
| 3cqe | P91 | Wee1-like protein kinase | 2.7.10.2 | 0.480 | |
| 1hk4 | T44 | Serum albumin | / | 0.477 | |
| 2pun | ACP | Methylthioribose kinase | 2.7.1.100 | 0.476 | |
| 3x0a | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.476 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.473 | |
| 4f1m | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.472 | |
| 4o4f | ATP | Kinase | / | 0.472 | |
| 2bak | AQZ | Mitogen-activated protein kinase 14 | / | 0.471 | |
| 2w5a | ADP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.471 | |
| 4a9y | AQZ | Mitogen-activated protein kinase 14 | / | 0.471 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.470 | |
| 3ba6 | AN2 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.468 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.467 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.467 | |
| 2cdc | NAP | Glucose 1-dehydrogenase | / | 0.466 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.466 | |
| 5ckw | ANP | Uncharacterized protein | / | 0.466 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 3dko | IHZ | Ephrin type-A receptor 7 | 2.7.10.1 | 0.464 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.464 | |
| 1ezf | IN0 | Squalene synthase | 2.5.1.21 | 0.463 | |
| 3iw8 | HIZ | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.463 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.462 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 2q70 | DC8 | Estrogen receptor | / | 0.461 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.460 | |
| 3eej | 53R | Uncharacterized protein | / | 0.460 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.460 | |
| 1e2j | THM | Thymidine kinase | / | 0.458 | |
| 3n2e | OSA | Shikimate kinase | 2.7.1.71 | 0.458 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.458 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.458 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.457 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3tpt | ADP | Serine/threonine-protein kinase toxin HipA | / | 0.457 | |
| 5bvw | 1N1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.457 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 2pup | ADP | Methylthioribose kinase | 2.7.1.100 | 0.456 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.456 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.456 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.455 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.455 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.455 | |
| 3tdl | 11D | Serum albumin | / | 0.455 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.455 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.453 | |
| 3hx3 | RET | Retinaldehyde-binding protein 1 | / | 0.453 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.453 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.452 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.452 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.452 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3fzt | 4JZ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.451 | |
| 3vi7 | CBD | Hematopoietic prostaglandin D synthase | / | 0.451 | |
| 3zlm | ANP | Adenosine monophosphate-protein transferase NmFic | 2.7.7.n1 | 0.451 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.451 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.450 | |
| 1zyd | ATP | eIF-2-alpha kinase GCN2 | / | 0.450 | |
| 2ewa | SB2 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 2pl0 | STI | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 3htj | ET | EbrA repressor | / | 0.450 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.450 | |
| 3zs5 | SB2 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3zsg | T75 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 1fr8 | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.449 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.449 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.449 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3cr7 | PPS | Adenylyl-sulfate kinase | 2.7.1.25 | 0.449 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.449 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.449 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.449 | |
| 5kf2 | COA | Predicted acetyltransferase | / | 0.449 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.448 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.448 | |
| 2jbl | SMA | Reaction center protein L chain | / | 0.448 | |
| 2p4i | MR9 | Angiopoietin-1 receptor | 2.7.10.1 | 0.448 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.448 | |
| 3q2m | CKI | Spectinomycin phosphotransferase | / | 0.448 | |
| 4gkh | 0J9 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.448 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 2rab | NAD | Glutathione amide reductase | / | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.447 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1jxz | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.446 | |
| 2xnm | WGZ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.446 | |
| 3eel | 53T | Uncharacterized protein | / | 0.446 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.446 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.446 | |
| 4f0f | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.446 | |
| 4qij | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.446 | |
| 1kyz | FER | Caffeic acid 3-O-methyltransferase | 2.1.1.68 | 0.445 | |
| 1ly3 | COG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.445 | |
| 2oh4 | GIG | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.445 | |
| 2w5b | AGS | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.445 | |
| 2xkd | T3M | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.445 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.445 | |
| 3be2 | RAJ | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.445 | |
| 3iss | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.445 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.445 | |
| 3n65 | XFJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 3p9t | TCL | Repressor | / | 0.445 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4aos | NAP | Steroid monooxygenase | / | 0.445 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.444 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1sir | NBC | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.444 | |
| 2bns | MST | Reaction center protein L chain | / | 0.444 | |
| 3aba | FLI | Cytochrome P450 | / | 0.444 | |
| 3d5w | ADP | Serine/threonine-protein kinase PLK | / | 0.444 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.444 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3ue4 | DB8 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.444 | |
| 3x06 | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.444 | |
| 4lb2 | DM5 | Serum albumin | / | 0.444 | |
| 1iah | ADP | Transient receptor potential cation channel subfamily M member 7 | 2.7.11.1 | 0.443 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 2io6 | 330 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 2q6h | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.443 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.443 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.443 | |
| 3cd2 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3cse | N22 | Uncharacterized protein | / | 0.443 | |
| 3rl3 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.443 | |
| 3tub | FPU | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.443 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.443 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2bil | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 2c9d | PHR | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2ocf | EST | Estrogen receptor | / | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 3fzs | B96 | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.442 | |
| 3tfn | 2CJ | Dehydrosqualene synthase | / | 0.442 | |
| 4afe | GGY | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2pui | ADP | Methylthioribose kinase | 2.7.1.100 | 0.441 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.441 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4ffm | ADP | Uncharacterized protein | / | 0.441 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.441 | |
| 4v01 | 0LI | Fibroblast growth factor receptor 1 (Fms-related tyrosine kinase 2, Pfeiffer syndrome), isoform CRA_b | / | 0.441 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1p16 | GTP | mRNA-capping enzyme subunit alpha | 2.7.7.50 | 0.440 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 1q3g | UDA | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.440 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 2og8 | 1N8 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.440 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.440 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.440 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.440 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.440 | |
| 4h98 | 14Q | Uncharacterized protein | / | 0.440 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 4ztv | TA7 | Anthranilate phosphoribosyltransferase | / | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |