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 |
|---|---|---|---|
| 4hld | 16T | Thymidylate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4hld | 16T | Thymidylate kinase | / | 1.000 | |
| 4gsy | 0Y5 | Thymidylate kinase | / | 0.727 | |
| 4hej | 14D | Thymidylate kinase | / | 0.582 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.514 | |
| 3l05 | SN0 | N-acetylornithine carbamoyltransferase | 2.1.3.9 | 0.509 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.498 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.497 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.496 | |
| 2ejz | SAH | Diphthine synthase | / | 0.491 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 3ele | PLP | Aminotransferase | / | 0.485 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.482 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.479 | |
| 4dch | 4DC | Glucokinase | 2.7.1.2 | 0.478 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.475 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.473 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.473 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.471 | |
| 1dgh | NDP | Catalase | 1.11.1.6 | 0.471 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.470 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.470 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.468 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.467 | |
| 1el4 | CTZ | Obelin | / | 0.466 | |
| 1map | KET | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.466 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.465 | |
| 3bsy | ACO | UDP-N-acetylbacillosamine N-acetyltransferase | 2.3.1.203 | 0.464 | |
| 3lm1 | LEC | Agglutinin alpha chain | / | 0.464 | |
| 2obx | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | 2.5.1.78 | 0.463 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.462 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.462 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.462 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.462 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.460 | |
| 1ahg | TYR_PLP | Aspartate aminotransferase | 2.6.1.1 | 0.459 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.459 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.459 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3p0e | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.459 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.458 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.458 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.457 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.457 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.456 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.456 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.455 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.455 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.454 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.454 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.454 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.454 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.454 | |
| 1fml | RTL | Retinol dehydratase | / | 0.453 | |
| 3imx | B84 | Glucokinase | 2.7.1.2 | 0.453 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.453 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.453 | |
| 1z4i | UMP | 5'(3')-deoxyribonucleotidase, mitochondrial | 3.1.3 | 0.452 | |
| 2tsr | UMP | Thymidylate synthase | 2.1.1.45 | 0.452 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.452 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 4g1c | CNA | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.452 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 1jf2 | CZH | Obelin | / | 0.451 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2poq | ISD | Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase | 1.3.1.20 | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.450 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3euf | BAU | Uridine phosphorylase 1 | / | 0.450 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.450 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.449 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.449 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 1maq | PGU | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.448 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.448 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.448 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.447 | |
| 2bxo | OPB | Serum albumin | / | 0.447 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3nhl | YTR | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.447 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 4cw5 | FMN | DfnA | / | 0.447 | |
| 5f12 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.447 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.446 | |
| 4lb2 | DM5 | Serum albumin | / | 0.446 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.445 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1nzy | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.445 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.445 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.445 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.445 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.445 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.444 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.444 | |
| 3r7m | SUZ | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.444 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1uhj | CZB | Aequorin-2 | / | 0.443 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.443 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.443 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4iix | 1EG | Microcin C7 self-immunity protein MccF | / | 0.443 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.443 | |
| 4zas | TYD | CalS13 | / | 0.443 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.442 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.442 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.442 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.442 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 1c7o | PPG | Hemolysin | / | 0.441 | |
| 1wpg | ADP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.441 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.441 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.441 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.440 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 |