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 |
|---|---|---|---|
| 3i9k | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3i9k | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 1.000 | |
| 2hct | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.518 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.495 | |
| 3i9j | NFD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.494 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.488 | |
| 3zwx | AV1 | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.479 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.477 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.473 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.471 | |
| 3zwo | G2Q | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase | 3.2.2.6 | 0.469 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.468 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.468 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.467 | |
| 3dzj | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.466 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.465 | |
| 4phl | PIL | Phosphodiesterase | / | 0.465 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.464 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 3dge | ADP | Sensor histidine kinase | / | 0.464 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.463 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.462 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.459 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.458 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.458 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.457 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.456 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.456 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.455 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.455 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.454 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.454 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.454 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.453 | |
| 2wnb | C5P | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 | 2.4.99.4 | 0.453 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.453 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.453 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.453 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.453 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.452 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.452 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.451 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.451 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.451 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.451 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.451 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.451 | |
| 4a7y | NHF | Aldos-2-ulose dehydratase | / | 0.451 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.451 | |
| 5cho | FAD | Flavin reductase | / | 0.451 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2j7d | GI1 | Beta-glucosidase A | 3.2.1.21 | 0.450 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.450 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.450 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.449 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.449 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.449 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.449 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.449 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.449 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.449 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.449 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2po3 | T4K | 4-dehydrase | / | 0.448 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2y4s | BCD | Limit dextrinase | / | 0.448 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3i12 | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.448 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4ca8 | 3ES | Angiotensin-converting enzyme | 3.4.15.1 | 0.448 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.448 | |
| 1fml | RTL | Retinol dehydratase | / | 0.447 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.447 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.447 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.447 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 4nqg | CZH | Mitrocomin | / | 0.447 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.446 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.446 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.446 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.446 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.446 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.445 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.445 | |
| 2aov | C2M | Histamine N-methyltransferase | 2.1.1.8 | 0.445 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.445 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.445 | |
| 1el4 | CTZ | Obelin | / | 0.444 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.444 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.444 | |
| 2fzb | TOL | Aldose reductase | 1.1.1.21 | 0.444 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.444 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.444 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.444 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.444 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.444 | |
| 1frb | ZST | Aldose reductase-related protein 2 | / | 0.443 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.443 | |
| 1s36 | CEI | Obelin | / | 0.443 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.443 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.443 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.443 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.443 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.443 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.442 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2gl0 | ADN | Uncharacterized protein | / | 0.442 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3q1k | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.442 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.442 | |
| 1e2n | RCA | Thymidine kinase | / | 0.441 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.441 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.441 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.441 | |
| 5dsy | UHB | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.441 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.440 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 2o8j | SAH | Histone-lysine N-methyltransferase EHMT2 | / | 0.440 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.440 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.440 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 |