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 |
|---|---|---|---|
| 4fkx | CDP | Nucleoside diphosphate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fkx | CDP | Nucleoside diphosphate kinase | / | 1.000 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.608 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.589 | |
| 1wkl | ATP | Nucleoside diphosphate kinase | / | 0.566 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.563 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.562 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.561 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.558 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.544 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.544 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.542 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.531 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.531 | |
| 1lwx | AZD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.523 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.518 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.512 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.502 | |
| 2dy9 | ADP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.486 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 4ork | GDP | Bifunctional AAC/APH | 2.3.1 | 0.485 | |
| 3b9l | AZZ | Serum albumin | / | 0.482 | |
| 5iqd | GNP | Bifunctional AAC/APH | 2.3.1 | 0.481 | |
| 4die | C5P | Cytidylate kinase | / | 0.475 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.472 | |
| 4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.472 | |
| 5iqa | GNP | Bifunctional AAC/APH | 2.3.1 | 0.472 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.470 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.470 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.469 | |
| 2dxe | GDP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.469 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.469 | |
| 1r8q | AFB | Cytohesin-2 | / | 0.467 | |
| 1r8q | AFB | ADP-ribosylation factor 1 | / | 0.467 | |
| 3vi7 | CBD | Hematopoietic prostaglandin D synthase | / | 0.466 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.466 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.465 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.464 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.464 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.464 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3wth | IM4 | Acetylcholine-binding protein | / | 0.463 | |
| 4bgb | ADP | Predicted molecular chaperone distantly related to HSP70-fold metalloproteases | / | 0.462 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.460 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.458 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.458 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3gie | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.458 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.457 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.457 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.456 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.454 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.454 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.454 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.454 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.454 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.453 | |
| 3up0 | D7S | aceDAF-12 | / | 0.453 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.453 | |
| 2qo7 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.452 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.452 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.452 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.452 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.452 | |
| 2giu | FBR | Estrogen receptor beta | / | 0.451 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.451 | |
| 2x0e | TYD | WsaF | / | 0.451 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.450 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 1a8t | 061 | Metallo-beta-lactamase type 2 | / | 0.449 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1nen | DNT | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.449 | |
| 1nen | DNT | Succinate dehydrogenase cytochrome b556 subunit | / | 0.449 | |
| 1t76 | DHT | Androgen receptor | / | 0.449 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.449 | |
| 3arv | SAU | Chitinase A | / | 0.449 | |
| 3ql3 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.449 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.448 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.448 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.448 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.448 | |
| 4kxl | 6C6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.448 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.448 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.448 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.447 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.447 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.447 | |
| 3tfj | THG | Dimethylsulfonioproprionate demethylase DmdA | 2.1.1.269 | 0.447 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1mx0 | ANP | Type 2 DNA topoisomerase 6 subunit B | / | 0.446 | |
| 2g44 | T3O | Estrogen receptor | / | 0.446 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 2j7y | E3O | Estrogen receptor beta | / | 0.446 | |
| 2pv7 | NAD | T-protein | 1.3.1.12 | 0.446 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.446 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.446 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2kce | D16 | Thymidylate synthase | / | 0.445 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.445 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.445 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.445 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.445 | |
| 7dfr | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.444 | |
| 1uyi | PUZ | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2vcw | ZZA | Hematopoietic prostaglandin D synthase | / | 0.444 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.444 | |
| 3up3 | XCA | aceDAF-12 | / | 0.444 | |
| 1iid | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.443 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.443 | |
| 1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.443 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.443 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.443 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.443 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 4r7u | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.443 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.443 | |
| 5iqh | GNP | Bifunctional AAC/APH | 2.3.1 | 0.443 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.442 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4l8u | 9AZ | Serum albumin | / | 0.442 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.442 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.442 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.441 | |
| 1tdu | DUR | Thymidylate synthase | / | 0.441 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.441 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.441 | |
| 2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.441 | |
| 3gep | 24H | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.441 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3k14 | 535 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.441 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.441 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.441 | |
| 4k37 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.441 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.441 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1bcp | ATP | Pertussis toxin subunit 4 | / | 0.440 | |
| 1bcp | ATP | Pertussis toxin subunit 5 | / | 0.440 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1dre | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1e4g | ATP | Cell division protein FtsA | / | 0.440 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2b1z | 17M | Estrogen receptor | / | 0.440 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2g8a | UMP | Thymidylate synthase | / | 0.440 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.440 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2jiz | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3tq8 | TOP | Dihydrofolate reductase | / | 0.440 | |
| 5iqf | GDP | Bifunctional AAC/APH | 2.3.1 | 0.440 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.440 |