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 |
|---|---|---|---|
| 4daj | 0HK | Muscarinic acetylcholine receptor M3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4daj | 0HK | Muscarinic acetylcholine receptor M3 | / | 1.000 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.662 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.611 | |
| 4u15 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.586 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.556 | |
| 5dsg | 0HK | Muscarinic acetylcholine receptor M4 | / | 0.542 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.502 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.493 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.491 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.489 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.487 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.486 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 3bur | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.468 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.467 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.463 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.462 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.460 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.460 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.459 | |
| 3eku | CY9 | Actin-5C | / | 0.459 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.459 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.458 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 3c1o | NAP | Eugenol synthase | / | 0.457 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4dya | 0MF | Nucleoprotein | / | 0.457 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.457 | |
| 1s36 | CEI | Obelin | / | 0.456 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1c7o | PPG | Hemolysin | / | 0.454 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.453 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.453 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.452 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.450 | |
| 4htx | 19F | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.450 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.450 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.450 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 3hgg | CHD | CmeR | / | 0.449 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.448 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.446 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3bmq | AX5 | Pteridine reductase | / | 0.445 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.445 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.445 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.444 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.444 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.444 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.444 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.443 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1qv0 | CZH | Obelin | / | 0.442 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.441 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.440 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.440 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.440 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4mm9 | FVX | Na(+):neurotransmitter symporter (Snf family) | / | 0.440 |