sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1w2g | THM | Thymidylate kinase | 2.7.4.9 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1w2g | THM | Thymidylate kinase | 2.7.4.9 | 1.000 | |
| 1n5i | TMP | Thymidylate kinase | 2.7.4.9 | 0.559 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.494 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.487 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.486 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.481 | |
| 3m3z | 3F5 | Heat shock cognate 71 kDa protein | / | 0.481 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.478 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.478 | |
| 1ndy | FR3 | Adenosine deaminase | 3.5.4.4 | 0.475 | |
| 2r7n | ADP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.475 | |
| 1a4l | DCF | Adenosine deaminase | 3.5.4.4 | 0.474 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.474 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.473 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.471 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.469 | |
| 4ug9 | 1EW | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.469 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.468 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.468 | |
| 5aqz | SGV | Heat shock 70 kDa protein 1A | / | 0.468 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.467 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.467 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.466 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.465 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.464 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 0.464 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.464 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.463 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.462 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.462 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.462 | |
| 4ug7 | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.462 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.461 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.461 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.459 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.458 | |
| 3dh0 | SAM | Uncharacterized protein | / | 0.458 | |
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.458 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.458 | |
| 3pbz | F02 | Endothiapepsin | 3.4.23.22 | 0.458 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.457 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.457 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.457 | |
| 3pch | CHB | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.457 | |
| 3six | GDP | Nodulation protein Z | / | 0.457 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 1p4a | PCP | Pur operon repressor | / | 0.456 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.456 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.456 | |
| 3pi0 | F91 | Endothiapepsin | 3.4.23.22 | 0.455 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.455 | |
| 1uk1 | FRQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.454 | |
| 2yoh | WMJ | Thymidylate kinase | / | 0.454 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.454 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.454 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4kxl | 6C6 | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | / | 0.454 | |
| 5ccy | TMP | Polymerase acidic protein | / | 0.454 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.453 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.453 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.453 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.453 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.453 | |
| 1y56 | FMN | Uncharacterized protein | / | 0.452 | |
| 1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.452 | |
| 3mcy | ZH1 | FimH | / | 0.452 | |
| 4zob | LGC | Lin1840 protein | / | 0.452 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.451 | |
| 2rcw | AAI | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.451 | |
| 3oxk | 5GP | Histidine triad nucleotide-binding protein | 3 | 0.451 | |
| 1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.450 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.450 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.450 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.449 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.449 | |
| 2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.449 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.448 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.448 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.447 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.447 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.446 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.446 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.446 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.446 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.445 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.445 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.445 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.445 | |
| 1hk5 | T44 | Serum albumin | / | 0.444 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 2yof | 74W | Thymidylate kinase | / | 0.444 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.444 | |
| 1ryd | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.443 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.443 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.443 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.443 | |
| 1e2n | RCA | Thymidine kinase | / | 0.442 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.442 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4ivr | N50 | Thymidine kinase | / | 0.442 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.442 | |
| 2e93 | B29 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3ele | PLP | Aminotransferase | / | 0.441 | |
| 3icz | PB6 | Farnesyl pyrophosphate synthase | / | 0.441 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.441 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4c8e | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.440 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 4oew | 5IO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.440 |