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 |
|---|---|---|---|
| 1c8k | CPB | Glycogen phosphorylase, muscle form | 2.4.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1c8k | CPB | Glycogen phosphorylase, muscle form | 2.4.1.1 | 1.000 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.508 | |
| 1vc9 | ATP | Diadenosine hexaphosphate hydrolase | 3.6.1.61 | 0.496 | |
| 4zs4 | ATP | Myosin heavy chain kinase A | 2.7.11.7 | 0.496 | |
| 2ycx | P32 | Beta-1 adrenergic receptor | / | 0.496 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.492 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.490 | |
| 3q1k | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.489 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.484 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.482 | |
| 4ewv | APC | 4-substituted benzoates-glutamate ligase GH3.12 | 6.3.2 | 0.482 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.480 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.480 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.479 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 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 | 0.476 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.475 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.475 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.475 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.475 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.474 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.474 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.474 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.473 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.472 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.472 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.472 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.471 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.470 | |
| 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 | 0.469 | |
| 4kn2 | LYA | Folate receptor beta | / | 0.469 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.468 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.468 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.466 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.465 | |
| 1waj | 5GP | DNA-directed DNA polymerase | / | 0.465 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.465 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4bis | 8HQ | Lysine-specific demethylase 4A | 1.14.11 | 0.465 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.463 | |
| 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 | 0.463 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.463 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.462 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.461 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.461 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.461 | |
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.460 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.460 | |
| 1fwy | UD1 | Bifunctional protein GlmU | / | 0.459 | |
| 2ycw | CAU | Beta-1 adrenergic receptor | / | 0.459 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3nya | JTZ | Beta-2 adrenergic receptor | / | 0.458 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.457 | |
| 3ebi | BEY | M1 family aminopeptidase | 3.4.11 | 0.457 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.457 | |
| 1clq | GDP | DNA-directed DNA polymerase | / | 0.456 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.456 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.456 | |
| 4phl | PIL | Phosphodiesterase | / | 0.456 | |
| 1mdl | SMN | Mandelate racemase | / | 0.455 | |
| 4da0 | GNG | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.455 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.455 | |
| 3gg2 | UGA | Sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family | / | 0.454 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.454 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.454 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.454 | |
| 1vft | DCS | Alanine racemase | / | 0.453 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.453 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.453 | |
| 4zme | ADN | Myosin heavy chain kinase A | 2.7.11.7 | 0.453 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 3ugr | IMN | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 1rkp | IBM | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.451 | |
| 1sm2 | STU | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.451 | |
| 1vrq | FMN | Subunit alpha of sarocosine oxidase | / | 0.451 | |
| 1vrq | FMN | Subunit beta of sarcosine oxidase | / | 0.451 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.451 | |
| 4k5o | 1OT | M1 family aminopeptidase | 3.4.11 | 0.451 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.451 | |
| 1ih7 | GMP | DNA-directed DNA polymerase | / | 0.450 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.450 | |
| 3iw8 | HIZ | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.450 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.449 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.449 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.449 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.449 | |
| 3uxe | 465 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.449 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.449 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.449 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.449 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.449 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.448 | |
| 1p72 | THM | Thymidine kinase | / | 0.448 | |
| 2v8p | CDP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.448 | |
| 4bqu | CLR | Japanin | / | 0.448 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.448 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.448 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.447 | |
| 2yay | DUP | DUTPase | / | 0.447 | |
| 3bur | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.447 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.446 | |
| 2iuz | D1H | Endochitinase B1 | 3.2.1.14 | 0.446 | |
| 2y4s | BCD | Limit dextrinase | / | 0.446 | |
| 2z2w | 770 | Wee1-like protein kinase | 2.7.10.2 | 0.446 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3ufg | ATP | Glycine--tRNA ligase alpha subunit | / | 0.446 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.445 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.445 | |
| 2y03 | 5FW | Beta-1 adrenergic receptor | / | 0.445 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.445 | |
| 3uaw | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 3zpq | XF5 | Beta-1 adrenergic receptor | / | 0.445 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.445 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.444 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.444 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.444 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.444 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.444 | |
| 4ogk | THM | Uridine phosphorylase | 2.4.2.3 | 0.444 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1qk3 | 5GP | Hypoxanthine-guanine-xanthine phosphoribosyltransferase | 2.4.2.22 | 0.443 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.443 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.443 | |
| 2c97 | JCL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2clh | F19 | Tryptophan synthase alpha chain | / | 0.443 | |
| 2ql6 | TIZ | Nicotinamide riboside kinase 1 | / | 0.443 | |
| 2xjc | 5GP | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.443 | |
| 3cui | X4S | Exoglucanase/xylanase | 3.2.1.91 | 0.443 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.443 | |
| 3wd3 | A1L | Chitinase B | 3.2.1.14 | 0.443 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.443 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1isg | AGS | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 | 0.442 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.442 | |
| 2q0g | UPU | Poly(A) polymerase, putative | / | 0.442 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3azz | LGC | Laminarinase | / | 0.442 | |
| 3gyn | B42 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4l34 | 1VG | Tankyrase-2 | 2.4.2.30 | 0.442 | |
| 4rel | KMP | Glycosyltransferase | / | 0.442 | |
| 5e9e | ANP | Myosin heavy chain kinase A | 2.7.11.7 | 0.442 | |
| 2j4d | MHF | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.441 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.441 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.441 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 3pdt | ADP | Myosin heavy chain kinase A | 2.7.11.7 | 0.441 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4gv8 | DUP | DUTPase | / | 0.441 | |
| 4ho6 | UPG | Glucose-1-phosphate thymidylyltransferase | / | 0.441 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.441 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.441 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.441 | |
| 4gbr | CAU | Beta-2 adrenergic receptor | / | 0.441 | |
| 1el4 | CTZ | Obelin | / | 0.440 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 2j62 | GSZ | O-GlcNAcase NagJ | / | 0.440 | |
| 2vqs | BVD | Deoxynucleoside kinase | / | 0.440 | |
| 2w5b | AGS | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.440 | |
| 3b9g | IMH | IAG-nucleoside hydrolase | / | 0.440 | |
| 3dwb | RDF | Endothelin-converting enzyme 1 | 3.4.24.71 | 0.440 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.440 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3l9n | L9N | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3nhy | A7B | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.440 | |
| 4i9q | XG4 | DNA-directed DNA polymerase | / | 0.440 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 2rh1 | CAU | Beta-2 adrenergic receptor | / | 0.440 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.440 |