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 |
|---|---|---|---|
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 1.000 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.489 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 4ej4 | EJ4 | Delta-type opioid receptor | / | 0.480 | |
| 2qju | DSM | Na(+):neurotransmitter symporter (Snf family) | / | 0.479 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.478 | |
| 3gxo | MQA | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.476 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.476 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.473 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.473 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.472 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.472 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.471 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.471 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.470 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.470 | |
| 3qly | 55V | Uncharacterized protein | / | 0.468 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.467 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.467 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.467 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.466 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 1w2g | THM | Thymidylate kinase | 2.7.4.9 | 0.464 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.464 | |
| 1qk3 | 5GP | Hypoxanthine-guanine-xanthine phosphoribosyltransferase | 2.4.2.22 | 0.463 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.463 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.463 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.462 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.460 | |
| 1rx4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.460 | |
| 3gww | SFX | Na(+):neurotransmitter symporter (Snf family) | / | 0.460 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.460 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3upy | FOM | Oxidoreductase, putative | / | 0.459 | |
| 2r7n | ADP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.458 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1h48 | CDI | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.457 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.457 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.457 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.457 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2f3m | GTD | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.455 | |
| 3koz | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.455 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.454 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.454 | |
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.454 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.454 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.453 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.453 | |
| 4h0x | NAD | Iota toxin component Ia | / | 0.453 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.452 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.451 | |
| 1bl6 | SB6 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.450 | |
| 2qei | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.450 | |
| 3ggc | H26 | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.450 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4ivr | N50 | Thymidine kinase | / | 0.450 | |
| 1rej | B1L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.449 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.449 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.449 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.449 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.448 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.448 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4lb9 | EVP | Serum albumin | / | 0.448 | |
| 4x7w | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.448 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1e26 | GPB | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 3rga | LSB | Epoxide hydrolase LasB | 5.5.1 | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.446 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.446 | |
| 2vtq | LZA | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.446 | |
| 3hqd | ANP | Kinesin-like protein KIF11 | / | 0.446 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.446 | |
| 5dib | NAD | Betaine-aldehyde dehydrogenase | / | 0.446 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.445 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 1a8t | 061 | Metallo-beta-lactamase type 2 | / | 0.444 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.444 | |
| 1vza | UMP | Thymidylate synthase | / | 0.444 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.444 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.444 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.443 | |
| 1rzy | 5AS | Histidine triad nucleotide-binding protein 1 | 3 | 0.443 | |
| 2brh | DFW | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.443 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3lp2 | LP9 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.443 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.442 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.442 | |
| 3beg | ANP | SRSF protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.442 | |
| 4ug9 | 1EW | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.442 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2eau | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.441 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.441 | |
| 2igy | A2T | Plasmepsin 2 | / | 0.441 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.441 | |
| 3cse | N22 | Uncharacterized protein | / | 0.441 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.441 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.441 | |
| 4jlt | 8PR | Cytochrome P450 2B4 | 1.14.14.1 | 0.441 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.441 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 1rx6 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.440 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2v2v | V12 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.440 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.440 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.440 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.440 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.440 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.440 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.440 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.440 |