The default benchmark contains 95 targets selected from the DUD-E Targets list. The targets are presented and described here. You may generate your own benchmark or specialized crossdocking dataset using the Generate tab. Please reference DUD-E for more information regarding the targets. Specifically, see the DUDE wiki page for documentation and discussion.
| # | Target Name | DUD-E Receptor | Description | Ligands | Docking Receptor | Successful Dock | Average Min RMSD | Difficulty | Download |
| 1 | THB | 1Q4X (pdb) | Thyroid hormone receptor beta-1 | 14 | 1Q4X (pdb) | 100.0% | 0.68+/-0.16 | Easy | Successful All |
| 2 | WEE1 | 1X8B (pdb) | Serine/threonine-protein kinase WEE1 | 8 | 2IO6 (pdb) | 100.0% | 0.75+/-0.5 | Easy | Successful All |
| 3 | KITH | 2B8T (pdb) | Thymidine kinase | 2 | 2UZ3 (pdb) | 100.0% | 0.98+/-0.45 | Easy | Successful All |
| 4 | ADRB1 | 3ZPQ (pdb) | Beta-1 adrenergic receptor | 15 | 3ZPQ (pdb) | 100.0% | 1.02+/-0.49 | Easy | Successful All |
| 5 | MCR | 3VHU (pdb) | Mineralocorticoid receptor | 18 | 3VHU (pdb) | 100.0% | 0.61+/-0.27 | Easy | Successful All |
| 6 | GCR | 3K23 (pdb) | Glucocorticoid receptor | 17 | 3K23 (pdb) | 100.0% | 1.27+/-0.45 | Easy | Successful All |
| 7 | HMDH | 1HWJ (pdb) | HMG-CoA reductase | 19 | 3CDB (pdb) | 100.0% | 0.98+/-0.25 | Easy | Successful All |
| 8 | ADRB2 | 2RH1 (pdb) | Beta-2 adrenergic receptor | 9 | 2RH1 (pdb) | 100.0% | 1.04+/-0.46 | Easy | Successful All |
| 9 | PA2GA | 1DB5 (pdb) | Phospholipase A2 group IIA | 8 | 1KVO (pdb) | 100.0% | 1.14+/-0.59 | Easy | Successful All |
| 10 | NRAM | 1A4Q (pdb) | Neuraminidase | 12 | 1B9V (pdb) | 100.0% | 0.94+/-0.5 | Easy | Successful All |
| 11 | DEF | 1BSK (pdb) | Peptide deformylase | 10 | 1G2A (pdb) | 100.0% | 1.0+/-0.22 | Easy | Successful All |
| 12 | ANDR | 1Z95 (pdb) | Androgen Receptor | 92 | 3B68 (pdb) | 98.4% | 0.86+/-0.53 | Easy | Successful All |
| 13 | ESR2 | 1NDE (pdb) | Estrogen receptor beta | 32 | 1NDE (pdb) | 93.3% | 1.13+/-0.46 | Easy | Successful All |
| 14 | PRGR | 1E3K (pdb) | Progesterone receptor | 18 | 1SR7 (pdb) | 92.3% | 1.04+/-0.44 | Easy | Successful All |
| 15 | ESR1 | 1UOM (pdb) | Estrogen receptor alpha | 104 | 2AYR (pdb) | 90.4% | 1.61+/-2.28 | Easy | Successful All |
| 16 | FA10 | 2Y82 (pdb) | Coagulation factor X | 104 | 1NFU (pdb) | 90.2% | 1.22+/-0.6 | Easy | Successful All |
| 17 | XIAP | 3HL5 (pdb) | Inhibitor of apoptosis protein 3 | 21 | 3HL5 (pdb) | 90.0% | 1.39+/-0.88 | Easy | Successful All |
| 18 | KIF11 | 3L9H (pdb) | Kinesin-like protein 1 | 32 | 3L9H (pdb) | 88.9% | 1.57+/-1.8 | Easy | Successful All |
| 19 | RXRA | 1FBY (pdb) | Retinoid X receptor alpha | 42 | 1MV9 (pdb) | 88.2% | 1.18+/-0.92 | Easy | Successful All |
| 20 | GLCM | 2V3F (pdb) | Beta-glucocerebrosidase | 9 | 2XWE (pdb) | 85.7% | 1.31+/-0.53 | Easy | Successful All |
| 21 | RENI | 3VYE (pdb) | Renin | 46 | 2V12 (pdb) | 85.3% | 1.85+/-1.9 | Easy | Successful All |
| 22 | HIVRT | 1C1B (pdb) | Human immunodeficiency virus type 1 reverse transcriptase | 169 | 1C1B (pdb) | 85.1% | 1.72+/-1.78 | Easy | Successful All |
| 23 | TGFR1 | 3GXL (pdb) | TGF-beta receptor type I | 15 | 3GXL (pdb) | 81.8% | 1.7+/-1.71 | Easy | Successful All |
| 24 | MAPK2 | 3KGA (pdb) | MAP kinase-activated protein kinase 2 | 13 | 3M2W (pdb) | 81.8% | 1.99+/-1.76 | Easy | Successful All |
| 25 | UROK | 1OWD (pdb) | Urokinase-type plasminogen activator | 14 | 1U6Q (pdb) | 81.8% | 1.92+/-1.78 | Easy | Successful All |
| 26 | VGFR2 | 3EWH (pdb) | Vascular endothelial growth factor receptor 2 | 24 | 3EWH (pdb) | 80.0% | 1.94+/-1.84 | Easy | Successful All |
| 27 | PNPH | 2ON6 (pdb) | Purine nucleoside phosphorylase | 6 | 2ON6 (pdb) | 80.0% | 1.18+/-0.88 | Easy | Successful All |
| 28 | CAH2 | 1BNU (pdb) | Carbonic anhydrase II | 242 | 1CNW (pdb) | 79.7% | 1.61+/-1.41 | Easy | Successful All |
| 29 | GRIA2 | 4IGT (pdb) | Glutamate receptor ionotropic AMPA 2 | 84 | 1SYI (pdb) | 79.2% | 1.57+/-1.54 | Easy | Successful All |
| 30 | TRY1 | 1YP9 (pdb) | Trypsin I | 169 | 1YP9 (pdb) | 78.3% | inf+/-nan | Easy | Successful All |
| 31 | JAK2 | 4C61 (pdb) | Tyrosine-protein kinase JAK2 | 48 | 4C61 (pdb) | 77.4% | 1.91+/-1.59 | Easy | Successful All |
| 32 | FKB1A | 1BKF (pdb) | FK506-binding protein 1A | 26 | 2FKE (pdb) | 76.5% | 2.6+/-2.78 | Easy | Successful All |
| 33 | LKHA4 | 3FUK (pdb) | Leukotriene A4 hydrolase | 39 | 3CHP (pdb) | 76.5% | 1.64+/-1.24 | Easy | Successful All |
| 34 | THRB | 2CF8 (pdb) | Thrombin | 216 | 2CF8 (pdb) | 75.8% | 1.75+/-1.49 | Easy | Successful All |
| 35 | ROCK1 | 3D9V (pdb) | Rho-associated protein kinase 1 | 12 | 2ETK (pdb) | 75.0% | 1.53+/-1.19 | Easy | Successful All |
| 36 | PARP1 | 1UK0 (pdb) | Poly [ADP-ribose] polymerase-1 | 17 | 4L6S (pdb) | 75.0% | 2.28+/-1.94 | Easy | Successful All |
| 37 | PGH1 | 1IGX (pdb) | Cyclooxygenase-1 | 19 | 3KK6 (pdb) | 73.3% | 1.99+/-1.9 | Medium | Successful All |
| 38 | AKT1 | 3QKM (pdb) | Serine/threonine-protein kinase AKT | 11 | 3QKM (pdb) | 70.0% | 2.18+/-2.12 | Medium | Successful All |
| 39 | PLK1 | 4J52 (pdb) | Serine/threonine-protein kinase PLK1 | 10 | 4J52 (pdb) | 70.0% | 1.97+/-2.35 | Medium | Successful All |
| 40 | HDAC2 | 3MAX (pdb) | Histone deacetylase 2 | 3 | 3MAX (pdb) | 66.7% | 2.87+/-3.49 | Medium | Successful All |
| 41 | PPARA | 1K7L (pdb) | Peroxisome proliferator-activated receptor alpha | 15 | 1K7L (pdb) | 66.7% | 3.34+/-3.5 | Medium | Successful All |
| 42 | PDE5A | 1XP0 (pdb) | Phosphodiesterase 5A | 26 | 1XP0 (pdb) | 66.7% | 2.01+/-1.3 | Medium | Successful All |
| 43 | PPARD | 2J14 (pdb) | Peroxisome proliferator-activated receptor delta | 21 | 3D5F (pdb) | 66.7% | 2.64+/-2.22 | Medium | Successful All |
| 44 | FA7 | 4ISH (pdb) | Coagulation factor VII | 42 | 4NA9 (pdb) | 66.7% | 2.24+/-1.54 | Medium | Successful All |
| 45 | HIVPR | 1XL2 (pdb) | Human immunodeficiency virus type 1 protease | 394 | 1HVR (pdb) | 66.2% | 2.04+/-1.52 | Medium | Successful All |
| 46 | ABL1 | 1OPJ (pdb) | Tyrosine-protein kinase ABL | 39 | 3GVU (pdb) | 63.3% | 5.19+/-5.84 | Medium | Successful All |
| 47 | HS90A | 1UYH (pdb) | Heat shock protein HSP 90-alpha | 175 | 1UYH (pdb) | 63.1% | 2.26+/-1.98 | Medium | Successful All |
| 48 | HIVIN | 3NF7 (pdb) | Human immunodeficiency virus type 1 integrase | 8 | 3NF8 (pdb) | 62.5% | 2.13+/-1.60 | Medium | Successful All |
| 49 | HXK4 | 3GOI (pdb) | Hexokinase type IV | 24 | 3VF6 (pdb) | 61.5% | 3.02+/-2.18 | Medium | Successful All |
| 50 | ADA | 1NDV (pdb) | Adenosine deaminase | 15 | 1NDV (pdb) | 61.5% | 2.54+/-1.8 | Medium | Successful All |
| 51 | CDK2 | 1H00 (pdb) | Cyclin-dependent kinase 2 | 310 | 1URW (pdb) | 61.0% | 2.22+/-1.36 | Medium | Successful All |
| 52 | CSF1R | 2I0Y (pdb) | Macrophage colony stimulating factor receptor | 12 | 3DPK (pdb) | 60.0% | 2.75+/-2.61 | Medium | Successful All |
| 53 | MK14 | 2PUU (pdb) | MAP kinase p38 alpha | 176 | 2PUU (pdb) | 59.3% | 2.68+/-2.2 | Medium | Successful All |
| 54 | GRIK1 | 4DLD (pdb) | Glutamate receptor ionotropic kainate 1 | 23 | 2PBW (pdb) | 59.1% | 2.43+/-1.53 | Medium | Successful All |
| 55 | BRAF | 1UWH (pdb) | Serine/threonine-protein kinase B-raf | 46 | 1UWJ (pdb) | 58.1% | 2.58+/-2.04 | Medium | Successful All |
| 56 | PGH2 | 3HS7 (pdb) | Cyclooxygenase-2 | 30 | 3HS6 (pdb) | 57.9% | 2.24+/-1.58 | Medium | Successful All |
| 57 | DPP4 | 2I78 (pdb) | Dipeptidyl peptidase IV | 71 | 2I78 (pdb) | 57.6% | 2.56+/-2.17 | Medium | Successful All |
| 58 | MP2K1 | 3ZM4 (pdb) | Dual specificity mitogen-activated protein kinase kinase 1 | 8 | 3ZM4 (pdb) | 57.1% | 3.8+/-4.13 | Medium | Successful All |
| 59 | TRYB1 | 4A6L (pdb) | Tryptase beta-1 | 13 | 4A6L (pdb) | 57.1% | 6.16+/-6.03 | Medium | Successful All |
| 60 | ADA17 | 3G42 (pdb) | ADAM17 | 12 | 3LEA (pdb) | 54.5% | 3.5+/-3.4 | Medium | Successful All |
| 61 | LCK | 3B2W (pdb) | Tyrosine-protein kinase LCK | 32 | 3BYM (pdb) | 52.6% | 2.35+/-1.62 | Medium | Successful All |
| 62 | MK01 | 3I60 (pdb) | MAP kinase ERK2 | 69 | 3I60 (pdb) | 52.0% | 2.8+/-1.93 | Medium | Successful All |
| 63 | PTN1 | 2ZN7 (pdb) | Protein-tyrosine phosphatase 1B | 74 | 2ZN7 (pdb) | 50.7% | 3.16+/-2.89 | Medium | Successful All |
| 64 | PUR2 | 1NJS (pdb) | GAR transformylase | 9 | 4EW3 (pdb) | 50.0% | 2.78+/-2.58 | Medium | Successful All |
| 65 | MET | 2WKM (pdb) | Hepatocyte growth factor receptor | 49 | 2WKM (pdb) | 50.0% | 4.72+/-4.11 | Medium | Successful All |
| 66 | ACE | 2OC2 (pdb) | Angiotensin-converting enzyme | 8 | 3BKK (pdb) | 50.0% | 3.21+/-2.89 | Medium | Successful All |
| 67 | ACES | 1ZGB (pdb) | Acetylcholinesterase | 41 | 2CEK (pdb) | 50.0% | 2.2+/-1.92 | Medium | Successful All |
| 68 | AKT2 | 2X39 (pdb) | Serine/threonine-protein kinase AKT2 | 10 | 2X39 (pdb) | 50.0% | 3.19+/-2.11 | Medium | Successful All |
| 69 | HDAC8 | 3SFF (pdb) | Histone deacetylase 8 | 7 | 3SFH (pdb) | 50.0% | 2.83+/-2.49 | Medium | Successful All |
| 70 | TYSY | 1BID (pdb) | Thymidylate synthase | 11 | 1BID (pdb) | 50.0% | 3.74+/-3.51 | Medium | Successful All |
| 71 | FAK1 | 2JKM (pdb) | Focal adhesion kinase 1 | 21 | 2JKM (pdb) | 47.1% | 4.02+/-3.78 | Medium | Successful All |
| 72 | FABP4 | 1TOW (pdb) | Fatty acid binding protein adipocyte | 22 | 1G74 (pdb) | 46.7% | 2.73+/-1.66 | Medium | Successful All |
| 73 | FPPS | 2F94 (pdb) | Farnesyl diphosphate synthase | 30 | 2F94 (pdb) | 46.2% | 1.86+/-0.79 | Medium | Successful All |
| 74 | MMP13 | 3LJZ (pdb) | Matrix metalloproteinase 13 | 28 | 4JPA (pdb) | 45.5% | 4.63+/-3.9 | Medium | Successful All |
| 75 | DYR | 1MVT (pdb) | Dihydrofolate reductase | 11 | 1PD9 (pdb) | 45.5% | 3.06+/-2.25 | Medium | Successful All |
| 76 | ITAL | 1RD4 (pdb) | Leukocyte adhesion glycoprotein LFA-1 alpha | 13 | 1RD4 (pdb) | 41.7% | 3.25+/-1.94 | Medium | Successful All |
| 77 | MK10 | 2B1P (pdb) | c-Jun N-terminal kinase 3 | 59 | 2B1P (pdb) | 40.4% | 3.47+/-2.45 | Medium | Successful All |
| 78 | KIT | 1T46 (pdb) | Stem cell growth factor receptor | 6 | 1T46 (pdb) | 40.0% | 3.81+/-2.24 | Medium | Successful All |
| 79 | SRC | 3TZ7 (pdb) | Tyrosine-protein kinase SRC | 48 | 3TZ7 (pdb) | 37.1% | 3.27+/-2.43 | Medium | Successful All |
| 80 | IGF1R | 3I81 (pdb) | Insulin-like growth factor I receptor | 13 | 3NW5 (pdb) | 36.4% | 4.17+/-2.87 | Medium | Successful All |
| 81 | BACE1 | 3L5D (pdb) | Beta-secretase 1 | 262 | 3LPK (pdb) | 35.5% | 3.59+/-2.23 | Hard | Successful All |
| 82 | CP2C9 | 1R9O (pdb) | Cytochrome P450 2C9 | 3 | 1R9O (pdb) | 33.3% | 8.24+/-5.50 | Hard | Successful All |
| 83 | ALDR | 2HV5 (pdb) | Aldose reductase | 3 | 2HV5 (pdb) | 33.3% | 10.01+/-6.3 | Hard | Successful All |
| 84 | SAHH | 1LI4 (pdb) | Adenosylhomocysteinase | 3 | 1LI4 (pdb) | 33.3% | 11.45+/-7.9 | Hard | Successful All |
| 85 | AOFB | 1S3B (pdb) | Monoamine oxidase B | 3 | 1S3B (pdb) | 33.3% | 14.37+/-9.1 | Hard | Successful All |
| 86 | EGFR | 2ITZ (pdb) | Epidermal growth factor receptor erbB1 | 81 | 2ITZ (pdb) | 33.3% | 3.68+/-2.17 | Hard | Successful All |
| 87 | AMPC | 3GSG (pdb) | Beta-lactamase | 59 | 3GSG (pdb) | 30.6% | 3.0+/-1.5 | Hard | Successful All |
| 88 | PPARG | 3G9E (pdb) | Peroxisome proliferator-activated receptor gamma | 116 | 3G9E (pdb) | 29.4% | 4.11+/-2.59 | Hard | Successful All |
| 89 | PYGM | 1C8K (pdb) | Muscle glycogen phosphorylase | 18 | 3EBP (pdb) | 28.6% | 4.56+/-4.3 | Hard | Successful All |
| 90 | FNTA | 1KZO (pdb) | Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit | 23 | 3EU5 (pdb) | 28.6% | 5.25+/-2.82 | Hard | Successful All |
| 91 | PYRD | 1D3G (pdb) | Dihydroorotate dehydrogenase | 4 | 1D3G (pdb) | 25.0% | 4.52+/-3.03 | Very Hard | Successful All |
| 92 | CASP3 | 1RHJ (pdb) | Caspase-3 | 21 | 2CNK (pdb) | 11.1% | 4.58+/-1.93 | Very Hard | Successful All |
| 93 | CXCR4 | 3ODU (pdb) | C-X-C chemokine receptor type 4 | 4 | 3OE8 (pdb) | 0.0% | 2.71+/-0.49 | Very Hard | Successful All |
| 94 | AA2AR | 3EML (pdb) | Adenosine A2a receptor | 2 | 3EML (pdb) | 0.0% | 8.29+/-0.11 | Very Hard | Successful All |
| 95 | CP3A4 | 3NXU (pdb) | Cytochrome P450 3A4 | 7 | 3NXU (pdb) | 0.0% | 7.67+/-1.86 | Very Hard | Successful All |
Cross Docking Benchmark is provided by the Camacho Laboratory at University of Pittsburgh and is developed by Shayne Wierbowski of the University of Scranton and Jim Zheng of the University of Pittsburgh.
Scripts and website content © 2025 Shayne Wierbowski - University of Scranton. Website content © 2025 Jim Zheng - University of Pittsburgh. All rights reserved.