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 |
|---|---|---|---|
| 5dw0 | PLS | Tryptophan synthase beta chain 1 | 4.2.1.20 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5dw0 | PLS | Tryptophan synthase beta chain 1 | 4.2.1.20 | 1.000 | |
| 2clo | PLS | Tryptophan synthase beta chain | 4.2.1.20 | 0.618 | |
| 1kfj | PLS | Tryptophan synthase beta chain | 4.2.1.20 | 0.616 | |
| 2tys | PLT | Tryptophan synthase beta chain | 4.2.1.20 | 0.546 | |
| 2trs | PLS | Tryptophan synthase beta chain | 4.2.1.20 | 0.518 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.494 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.490 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.487 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.482 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.475 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.473 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.473 | |
| 2xk8 | 5R1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.471 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.470 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.470 | |
| 1e2j | THM | Thymidine kinase | / | 0.468 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.468 | |
| 3bx5 | 304 | Mitogen-activated protein kinase 14 | / | 0.467 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.466 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.465 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.465 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.464 | |
| 3nbv | ANP | Ketohexokinase | / | 0.462 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.461 | |
| 4aot | GW8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.461 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.460 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.460 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.459 | |
| 3e92 | G6A | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.458 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.458 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.458 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 2vwp | NDP | Glucose 1-dehydrogenase | / | 0.457 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.457 | |
| 4h3y | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.457 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 1i2c | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.456 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.456 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.456 | |
| 2qo7 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.454 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 5kbw | RBF | Riboflavin transporter RibU | / | 0.454 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.453 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 3qa2 | XNA | Ketohexokinase | / | 0.453 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.453 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 1u54 | ACP | Activated CDC42 kinase 1 | / | 0.452 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.452 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.452 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.451 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.451 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.451 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.451 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.451 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.451 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.450 | |
| 1v0p | PVB | Cell division control protein 2 homolog | 2.7.11.22 | 0.450 | |
| 2e9n | 76A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.450 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.450 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.450 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.450 | |
| 3vs2 | VSB | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.450 | |
| 4ft5 | H2K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.450 | |
| 5cns | CDP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.450 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.449 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.449 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 4ike | ADP | Adenylate kinase | / | 0.449 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.448 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.448 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.448 | |
| 4bie | IE6 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.448 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.448 | |
| 4cnz | ADP | Nitrogen regulatory protein P-II 1 | / | 0.448 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.448 | |
| 4xt5 | NAP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.448 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.448 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.447 | |
| 2vwx | 7X4 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.447 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.447 | |
| 4r8h | SP1 | cAMP-activated global transcriptional regulator CRP | / | 0.447 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.447 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.446 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.446 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.446 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.446 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.446 | |
| 2xnp | WCX | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.446 | |
| 5e8x | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.446 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.445 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.445 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.445 | |
| 2zb1 | GK4 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3zm4 | 22T | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.445 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.445 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.445 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4zhq | ACP | Tubulin tyrosine ligase | / | 0.445 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.444 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.444 | |
| 2q0u | LAB | Actin, alpha skeletal muscle | / | 0.444 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.444 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.444 | |
| 4o0u | ADN | Aurora kinase A | 2.7.11.1 | 0.444 | |
| 5e92 | ANP | TGF-beta receptor type-2 | 2.7.11.30 | 0.444 | |
| 1pg3 | PRX | Acetyl-coenzyme A synthetase | / | 0.443 | |
| 2ej2 | PPE | Branched-chain amino acid aminotransferase (IlvE) | / | 0.443 | |
| 2g97 | DGB | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.443 | |
| 2p2b | PRX | Acetyl-coenzyme A synthetase | / | 0.443 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.443 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3nta | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.443 | |
| 3uvp | 048 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.443 | |
| 4kgm | ATP | Uncharacterized protein | / | 0.443 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.442 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 2rl2 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.442 | |
| 2vx1 | 7X8 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.442 | |
| 2w5a | ADP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 3dt1 | P40 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.442 | |
| 3t9a | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.442 | |
| 3zw9 | T1G | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.442 | |
| 4u9a | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.441 | |
| 1rkd | ADP | Ribokinase | / | 0.441 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.441 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.441 | |
| 3tb9 | CDP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.441 | |
| 4aqc | 88A | Tyrosine-protein kinase JAK2 | / | 0.441 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4fsz | HK8 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 4yb7 | ATP | ATP phosphoribosyltransferase | / | 0.441 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.441 | |
| 5dkk | FMN | Predicted protein | / | 0.441 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.441 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.440 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.440 | |
| 2bn4 | NAP | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3ac5 | KZM | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.440 | |
| 4c59 | FEF | Cyclin-G-associated kinase | 2.7.11.1 | 0.440 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.440 | |
| 5fbh | TCR | Extracellular calcium-sensing receptor | / | 0.440 |