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 |
|---|---|---|---|
| 2wm3 | NFL | NmrA-like family domain-containing protein 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2wm3 | NFL | NmrA-like family domain-containing protein 1 | / | 1.000 | |
| 2wmd | ZZ0 | NmrA-like family domain-containing protein 1 | / | 0.560 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.516 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.502 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.496 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.492 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.488 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.484 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.483 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.482 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.481 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.478 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.477 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.477 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.477 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.476 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.473 | |
| 4nqg | CZH | Mitrocomin | / | 0.473 | |
| 2aov | C2M | Histamine N-methyltransferase | 2.1.1.8 | 0.472 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.471 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.471 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.469 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.469 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.468 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.468 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.466 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.466 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.466 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.465 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.465 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.463 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.463 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.463 | |
| 1el4 | CTZ | Obelin | / | 0.462 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.462 | |
| 4iah | 1DX | Alr2278 protein | / | 0.462 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.462 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.461 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.460 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.459 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.459 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.458 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.458 | |
| 1c7o | PPG | Hemolysin | / | 0.457 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.456 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.455 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.455 | |
| 3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.455 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 5a4w | QCT | Glutathione S-transferase F2 | 2.5.1.18 | 0.455 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.455 | |
| 5d5a | CAU | Beta-2 adrenergic receptor | / | 0.455 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 1zdw | FLV | Prenyltransferase | / | 0.454 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 4diq | PD2 | Ribosomal oxygenase 1 | / | 0.454 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.452 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.452 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.452 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.451 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4daj | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.450 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.447 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.447 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.446 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.446 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.446 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.446 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1s36 | CEI | Obelin | / | 0.445 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.445 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.445 | |
| 5d5b | CAU | Beta-2 adrenergic receptor | / | 0.445 | |
| 1e2n | RCA | Thymidine kinase | / | 0.444 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.444 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3esz | FMN | Flavodoxin | / | 0.444 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.444 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.443 | |
| 1oxo | IK2 | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.443 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.443 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.443 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.443 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.442 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3gb4 | D3M | DdmC | / | 0.442 | |
| 3lzz | GDP | Uncharacterized protein | / | 0.442 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.442 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.442 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.441 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.441 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.441 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.441 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4e31 | JHZ | Methyltransferase | / | 0.441 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.440 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.440 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.440 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.440 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.440 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.440 | |
| 2rh1 | CAU | Beta-2 adrenergic receptor | / | 0.440 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.440 | |
| 3nya | JTZ | Beta-2 adrenergic receptor | / | 0.440 |