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 |
|---|---|---|---|
| 4jq1 | NPS | Aldo-keto reductase family 1 member C2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4jq1 | NPS | Aldo-keto reductase family 1 member C2 | / | 1.000 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.625 | |
| 4jtr | IBP | Aldo-keto reductase family 1 member C2 | / | 0.616 | |
| 4jtr | IZP | Aldo-keto reductase family 1 member C2 | / | 0.603 | |
| 4jq2 | SUZ | Aldo-keto reductase family 1 member C2 | / | 0.593 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.593 | |
| 1ihi | IU5 | Aldo-keto reductase family 1 member C2 | / | 0.587 | |
| 4xo7 | ASD | Aldo-keto reductase family 1 member C2 | / | 0.582 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.578 | |
| 2ipj | FFA | Aldo-keto reductase family 1 member C2 | / | 0.567 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.559 | |
| 4l1x | STR | Aldo-keto reductase family 1 member C2 | / | 0.513 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.494 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.485 | |
| 3tfj | THG | Dimethylsulfonioproprionate demethylase DmdA | 2.1.1.269 | 0.479 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.477 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.477 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.477 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.476 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.476 | |
| 4n1g | CEI | Obelin | / | 0.473 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.472 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.471 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.471 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.471 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.471 | |
| 4bvh | OCZ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.470 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.469 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.469 | |
| 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 | 0.469 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.468 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.467 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.467 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.465 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.461 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4xwt | U5P | Ribonuclease J | / | 0.461 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1kuy | COT | Serotonin N-acetyltransferase | / | 0.459 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.459 | |
| 4iae | 1DX | Alr2278 protein | / | 0.459 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.458 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.457 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.457 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.457 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.456 | |
| 3ce0 | P34 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.456 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.456 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3f3y | 4OA | Bile salt sulfotransferase | 2.8.2.14 | 0.455 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.455 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.455 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.455 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.455 | |
| 1fml | RTL | Retinol dehydratase | / | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2vqo | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.454 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.454 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.453 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.453 | |
| 2pdx | ZST | Aldose reductase | 1.1.1.21 | 0.453 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.453 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.453 | |
| 1zdw | FLV | Prenyltransferase | / | 0.452 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.452 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.452 | |
| 1el4 | CTZ | Obelin | / | 0.451 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 2dv0 | ZST | Aldose reductase | 1.1.1.21 | 0.451 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.451 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.450 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.450 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.450 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.450 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.450 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.450 | |
| 4n1f | CZH | Obelin | / | 0.450 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.448 | |
| 1lke | DOG | Bilin-binding protein | / | 0.448 | |
| 1rxj | BNI | Streptavidin | / | 0.448 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.448 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.447 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.447 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.446 | |
| 3b82 | NAD | Exotoxin A | 2.4.2.36 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3ptz | UDX | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.446 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4hcy | 0YN | Transketolase | / | 0.446 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.446 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.445 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.445 | |
| 1qv0 | CZH | Obelin | / | 0.445 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.444 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.444 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.444 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.444 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.443 | |
| 4l6s | 1WQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 4phl | PIL | Phosphodiesterase | / | 0.443 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.443 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.443 | |
| 5dsy | UHB | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.443 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1n5v | NOM | ActVA 6 protein | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3gey | P34 | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.442 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.442 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.442 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3f6s | FMN | Flavodoxin | / | 0.441 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 5f12 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.441 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1swe | BTN | Streptavidin | / | 0.440 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.440 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2yhu | WHF | Pteridine reductase | / | 0.440 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.440 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.440 | |
| 4gd9 | BTN | Streptavidin | / | 0.440 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |