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 |
|---|---|---|---|
| 3e9s | TTT | Replicase polyprotein 1ab | 3.4.22 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3e9s | TTT | Replicase polyprotein 1ab | 3.4.22 | 1.000 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.510 | |
| 3mj5 | GRM | Replicase polyprotein 1a | 3.4.22 | 0.509 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.495 | |
| 3tza | TZG | Glutamate receptor 2 | / | 0.487 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.483 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.477 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.475 | |
| 4wxg | 2BO | Serine hydroxymethyltransferase | / | 0.474 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.473 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.472 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 2rdn | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.471 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.470 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.469 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.468 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.467 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.466 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.464 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.464 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.464 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.463 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.463 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.462 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.461 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.461 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.460 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.460 | |
| 4rel | KMP | Glycosyltransferase | / | 0.460 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.459 | |
| 2c97 | JCL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.458 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.458 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.458 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.457 | |
| 1ppj | ANY | Cytochrome b | / | 0.456 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.456 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.456 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.456 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.456 | |
| 3rzp | PRF | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.456 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.456 | |
| 1cq6 | PY4 | Aspartate aminotransferase | 2.6.1.1 | 0.455 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.455 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.455 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.455 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 3w0t | HPU | Lactoylglutathione lyase | 4.4.1.5 | 0.455 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.455 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.454 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.454 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.454 | |
| 1e2n | RCA | Thymidine kinase | / | 0.453 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.453 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.453 | |
| 4xo7 | ASD | Aldo-keto reductase family 1 member C2 | / | 0.453 | |
| 4ys0 | ADP | Protein translocase subunit SecA | / | 0.453 | |
| 1qy2 | IPZ | Major urinary protein 1 | / | 0.452 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.452 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.452 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.451 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.451 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.451 | |
| 5dp2 | NAP | CurF | / | 0.451 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.450 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.450 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.450 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.449 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.448 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.448 | |
| 1bl4 | AP1 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 1map | KET | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.447 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.447 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.447 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4phl | PIL | Phosphodiesterase | / | 0.447 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.446 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.446 | |
| 3rt8 | CWD | Glutamate receptor 3 | / | 0.446 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.446 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.445 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.445 | |
| 1q6n | P90 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.445 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 3p0e | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.445 | |
| 4f79 | P53 | Putative phospho-beta-glucosidase | / | 0.445 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.445 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.444 | |
| 1k8z | IAG | Tryptophan synthase alpha chain | / | 0.444 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.444 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.444 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 1fki | SB1 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1qs2 | NAD | Vip2Ac | / | 0.443 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.443 | |
| 2f6r | ACO | Bifunctional coenzyme A synthase | / | 0.443 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.443 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.443 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.443 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.442 | |
| 2clm | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.442 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.442 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.442 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1s9d | AFB | Cytohesin-2 | / | 0.441 | |
| 1s9d | AFB | ADP-ribosylation factor 1 | / | 0.441 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.441 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 1maq | PGU | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1syn | F89 | Thymidylate synthase | / | 0.440 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.440 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.440 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.440 |