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 |
|---|---|---|---|
| 2r1n | EPL | Phosphotriesterase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2r1n | EPL | Phosphotriesterase | / | 1.000 | |
| 2d2g | DZZ | Phosphotriesterase | / | 0.689 | |
| 1dpm | EBP | Parathion hydrolase | 3.1.8.1 | 0.550 | |
| 1xid | ASC | Xylose isomerase | 5.3.1.5 | 0.506 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.498 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.495 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.491 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.491 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.490 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.490 | |
| 4gd9 | BTN | Streptavidin | / | 0.490 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.486 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.480 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.478 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.477 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.477 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.476 | |
| 1rkp | IBM | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.475 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.474 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.472 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.471 | |
| 2fzb | TOL | Aldose reductase | 1.1.1.21 | 0.470 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.468 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.468 | |
| 4oma | LCS | Methionine gamma-lyase | / | 0.468 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.468 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.467 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.467 | |
| 2xnn | 430 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.465 | |
| 3a8i | C2F | Aminomethyltransferase | 2.1.2.10 | 0.465 | |
| 3x02 | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.465 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2z2w | 770 | Wee1-like protein kinase | 2.7.10.2 | 0.464 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.463 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.463 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.463 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.463 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.463 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.463 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.462 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.461 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.461 | |
| 3ccb | B2Y | Dipeptidyl peptidase 4 | / | 0.461 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.461 | |
| 4dya | 0MF | Nucleoprotein | / | 0.461 | |
| 1t9b | 1CS | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.460 | |
| 2g8n | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.460 | |
| 4kzl | 20D | Tankyrase-2 | 2.4.2.30 | 0.460 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.458 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.458 | |
| 1qv0 | CZH | Obelin | / | 0.457 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.457 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.457 | |
| 5d5a | CAU | Beta-2 adrenergic receptor | / | 0.457 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.456 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.456 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.456 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 4xmx | BES | Aminopeptidase N | 3.4.11.2 | 0.456 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.455 | |
| 2r86 | ATP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.455 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 4gvs | F4M | Methenyltetrahydromethanopterin cyclohydrolase | 3.5.4.27 | 0.455 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.455 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.454 | |
| 2vt4 | P32 | Beta-1 adrenergic receptor | / | 0.454 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.454 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.453 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.453 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 4nqg | CZH | Mitrocomin | / | 0.453 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.452 | |
| 1dtp | APU | Diphtheria toxin | / | 0.451 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.451 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.451 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.451 | |
| 3arz | I5I | Chitinase A | / | 0.451 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.451 | |
| 4l0t | 1V0 | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.450 | |
| 3arv | SAU | Chitinase A | / | 0.450 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.450 | |
| 3upy | FOM | Oxidoreductase, putative | / | 0.450 | |
| 1z4i | UMP | 5'(3')-deoxyribonucleotidase, mitochondrial | 3.1.3 | 0.449 | |
| 2idv | M7G | Eukaryotic translation initiation factor 4E-1 | / | 0.449 | |
| 3c6n | 2S8 | Protein TRANSPORT INHIBITOR RESPONSE 1 | / | 0.449 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4itx | IN5 | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.449 | |
| 4j7h | TRH | PCZA361.3 | / | 0.449 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.449 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.449 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.449 | |
| 1dls | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2c92 | TP6 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 3rl4 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.448 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.448 | |
| 4fkx | CDP | Nucleoside diphosphate kinase | / | 0.448 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.447 | |
| 1pd8 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 1swg | BTN | Streptavidin | / | 0.447 | |
| 2bak | AQZ | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.447 | |
| 4a9y | AQZ | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4ajg | F07 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2bxo | OPB | Serum albumin | / | 0.446 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 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 | 0.446 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.446 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.446 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.446 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.446 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.446 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.445 | |
| 2de4 | BPS | 2'-hydroxybiphenyl-2-sulfinate desulfinase | 3.13.1.3 | 0.445 | |
| 2f0y | 3MN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.445 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.445 | |
| 4kn2 | LYA | Folate receptor beta | / | 0.445 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.445 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1u70 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4bjc | RPB | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 4gts | 7TP | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.444 | |
| 4j7g | TRH | PCZA361.3 | / | 0.444 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1n08 | ADP | Riboflavin kinase | 2.7.1.26 | 0.443 | |
| 1rxj | BNI | Streptavidin | / | 0.443 | |
| 1sg0 | STL | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.443 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.443 | |
| 3qgi | 33F | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4i5x | FLF | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.443 | |
| 1eq2 | ADQ | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.442 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1zos | MTM | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | / | 0.442 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.442 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.442 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.442 | |
| 3tfj | THG | Dimethylsulfonioproprionate demethylase DmdA | 2.1.1.269 | 0.442 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 1xi2 | CB1 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.441 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.441 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 4l09 | 1UR | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.441 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 1r8q | AFB | Cytohesin-2 | / | 0.440 | |
| 1r8q | AFB | ADP-ribosylation factor 1 | / | 0.440 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2vax | CSC | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.440 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.440 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3p70 | ILE_PHE_GLU_PRO_PRO | Prothrombin | 3.4.21.5 | 0.440 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 | |
| 3pz3 | PZ3 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.440 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4gtt | 7TQ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 4hmh | F94 | Tankyrase-2 | 2.4.2.30 | 0.440 | |
| 4lsa | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.440 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.440 | |
| 4qii | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.440 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.440 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.440 |