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 |
|---|---|---|---|
| 2qcx | PF1 | Aminopyrimidine aminohydrolase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2qcx | PF1 | Aminopyrimidine aminohydrolase | / | 1.000 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.512 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.493 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.489 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.488 | |
| 2xls | NAP | Putative flavin-containing monooxygenase | / | 0.485 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.484 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.478 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.477 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.476 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.476 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.476 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.476 | |
| 2g0g | SP0 | Peroxisome proliferator-activated receptor gamma | / | 0.475 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.474 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.474 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.473 | |
| 4kxj | P34 | Nucleoprotein | / | 0.473 | |
| 1lke | DOG | Bilin-binding protein | / | 0.472 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.472 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.470 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.468 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.467 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.467 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.466 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.465 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.464 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.464 | |
| 2jji | 0QS | Endothiapepsin | 3.4.23.22 | 0.463 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.462 | |
| 2xvv | 9DN | Serum albumin | / | 0.462 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.462 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.461 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.461 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.461 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.461 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 5cuq | NSC | Genome polyprotein | / | 0.461 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.459 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3arv | SAU | Chitinase A | / | 0.458 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.458 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.457 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.457 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.457 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.457 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.456 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.456 | |
| 2vz0 | D64 | Pteridine reductase | / | 0.456 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2xlr | NAP | Putative flavin-containing monooxygenase | / | 0.456 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.456 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.456 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.456 | |
| 1e82 | M90 | Endothiapepsin | 3.4.23.22 | 0.455 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.455 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.455 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.455 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.455 | |
| 4hqv | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.455 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.454 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.454 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.454 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.453 | |
| 3gb4 | D3M | DdmC | / | 0.453 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.453 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.452 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.452 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.452 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.451 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.450 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.449 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 3w4k | 3LD | D-amino-acid oxidase | 1.4.3.3 | 0.449 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.449 | |
| 4eh8 | IRG | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2jjj | 0QS | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.448 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.448 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4iil | RBF | Membrane lipoprotein TpN38(b) | / | 0.448 | |
| 5fe1 | 12Q | Histone acetyltransferase KAT2B | 2.3.1.48 | 0.448 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1e92 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.447 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.447 | |
| 4hsh | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.447 | |
| 5dp2 | NAP | CurF | / | 0.447 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.446 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.446 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.446 | |
| 5iw4 | NAD | NADH pyrophosphatase | / | 0.446 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.445 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.445 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.445 | |
| 5ikq | JMS | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 1gvw | 0EM | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.444 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.444 | |
| 2xvw | 9NR | Serum albumin | / | 0.444 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.444 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.444 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.443 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.443 | |
| 2qjp | ANJ | Cytochrome b | / | 0.443 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.443 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.443 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.443 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.443 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2qhx | FE1 | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 4a16 | H34 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.442 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4yfy | 0FX | VioF | / | 0.442 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1l0o | ADP | Anti-sigma F factor | / | 0.441 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.441 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.441 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.441 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.441 | |
| 4dbu | BT9 | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 4ttj | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.441 | |
| 1e81 | M91 | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3gam | MXX | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.440 |