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 | HIVPR | 1XL2 (pdb) | Human immunodeficiency virus type 1 protease | 394 | 2I4U (pdb) | 34.7% | 5.38+/-3.93 | Hard | Successful All |
| 2 | CDK2 | 1H00 (pdb) | Cyclin-dependent kinase 2 | 310 | 3QQK (pdb) | 15.6% | 4.26+/-2.26 | Very Hard | Successful All |
| 3 | BACE1 | 3L5D (pdb) | Beta-secretase 1 | 262 | 4D89 (pdb) | 26.9% | 4.64+/-2.95 | Hard | Successful All |
| 4 | CAH2 | 1BNU (pdb) | Carbonic anhydrase II | 242 | 1BNU (pdb) | 48.1% | 2.69+/-2.01 | Medium | Successful All |
| 5 | THRB | 2ZG0 (pdb) | Thrombin | 216 | 2ZNK (pdb) | 62.5% | 2.53+/-2.36 | Medium | Successful All |
| 6 | MK14 | 3FC1 (pdb) | MAP kinase p38 alpha | 176 | 3GCQ (pdb) | 41.4% | 5.55+/-4.57 | Medium | Successful All |
| 7 | HS90A | 3RLP (pdb) | Heat shock protein HSP 90-alpha | 175 | 3RLP (pdb) | 44.3% | 3.57+/-2.84 | Medium | Successful All |
| 8 | HIVRT | 1C1B (pdb) | Human immunodeficiency virus type 1 reverse transcriptase | 169 | 1C1B (pdb) | 66.3% | 2.6+/-2.47 | Medium | Successful All |
| 9 | TRY1 | 1PPH (pdb) | Trypsin I | 169 | 1YP9 (pdb) | 58.3% | inf+/-nan | Medium | Successful All |
| 10 | PPARG | 1I7I (pdb) | Peroxisome proliferator-activated receptor gamma | 116 | 4EMA (pdb) | 16.2% | 6.1+/-3.45 | Very Hard | Successful All |
| 11 | FA10 | 2Y82 (pdb) | Coagulation factor X | 104 | 1NFU (pdb) | 64.6% | 2.78+/-2.78 | Medium | Successful All |
| 12 | ESR1 | 1SJ0 (pdb) | Estrogen receptor alpha | 104 | 2QE4 (pdb) | 59.6% | 3.17+/-3.0 | Medium | Successful All |
| 13 | ANDR | 1T65 (pdb) | Androgen Receptor | 92 | 4HLW (pdb) | 82.3% | 1.27+/-1.94 | Easy | Successful All |
| 14 | GRIA2 | 4F22 (pdb) | Glutamate receptor ionotropic AMPA 2 | 84 | 1SYI (pdb) | 66.2% | 2.25+/-1.88 | Medium | Successful All |
| 15 | EGFR | 1M17 (pdb) | Epidermal growth factor receptor erbB1 | 81 | 3IKA (pdb) | 19.4% | 5.67+/-2.81 | Very Hard | Successful All |
| 16 | PTN1 | 2ZMM (pdb) | Protein-tyrosine phosphatase 1B | 74 | 2ZMM (pdb) | 38.8% | 4.04+/-3.14 | Medium | Successful All |
| 17 | DPP4 | 2I78 (pdb) | Dipeptidyl peptidase IV | 71 | 2IIT (pdb) | 35.6% | 4.31+/-3.26 | Medium | Successful All |
| 18 | MK01 | 3I60 (pdb) | MAP kinase ERK2 | 69 | 3I60 (pdb) | 36.0% | 4.67+/-3.38 | Medium | Successful All |
| 19 | MK10 | 2EXC (pdb) | c-Jun N-terminal kinase 3 | 59 | 2ZDU (pdb) | 27.7% | 5.13+/-3.26 | Hard | Successful All |
| 20 | AMPC | 1L2S (pdb) | Beta-lactamase | 59 | 3GSG (pdb) | 11.1% | 4.38+/-1.92 | Very Hard | Successful All |
| 21 | MET | 3ZCL (pdb) | Hepatocyte growth factor receptor | 49 | 3ZCL (pdb) | 45.0% | 4.75+/-3.98 | Medium | Successful All |
| 22 | JAK2 | 4C61 (pdb) | Tyrosine-protein kinase JAK2 | 48 | 4C61 (pdb) | 45.2% | 3.78+/-2.9 | Medium | Successful All |
| 23 | SRC | 3F3V (pdb) | Tyrosine-protein kinase SRC | 48 | 3TZ7 (pdb) | 22.9% | 5.23+/-4.26 | Very Hard | Successful All |
| 24 | RENI | 3VYD (pdb) | Renin | 46 | 3VYD (pdb) | 64.7% | 2.46+/-2.22 | Medium | Successful All |
| 25 | BRAF | 3IDP (pdb) | Serine/threonine-protein kinase B-raf | 46 | 4FC0 (pdb) | 45.2% | 4.62+/-4.06 | Medium | Successful All |
| 26 | RXRA | 3FAL (pdb) | Retinoid X receptor alpha | 42 | 3OAP (pdb) | 70.6% | 1.99+/-1.65 | Medium | Successful All |
| 27 | FA7 | 1Z6J (pdb) | Coagulation factor VII | 42 | 1W0Y (pdb) | 45.8% | 3.88+/-3.36 | Medium | Successful All |
| 28 | ACES | 1ZGB (pdb) | Acetylcholinesterase | 41 | 1ZGB (pdb) | 25.0% | 3.84+/-2.34 | Hard | Successful All |
| 29 | ABL1 | 1OPJ (pdb) | Tyrosine-protein kinase ABL | 39 | 3PYY (pdb) | 60.0% | 5.98+/-6.56 | Medium | Successful All |
| 30 | LKHA4 | 3FH5 (pdb) | Leukotriene A4 hydrolase | 39 | 3U9W (pdb) | 41.2% | 4.74+/-3.96 | Medium | Successful All |
| 31 | KIF11 | 1Q0B (pdb) | Kinesin-like protein 1 | 32 | 2X7D (pdb) | 81.5% | 1.71+/-1.74 | Easy | Successful All |
| 32 | ESR2 | 3OMP (pdb) | Estrogen receptor beta | 32 | 1X78 (pdb) | 76.7% | 2.12+/-2.32 | Easy | Successful All |
| 33 | LCK | 2OG8 (pdb) | Tyrosine-protein kinase LCK | 32 | 2OG8 (pdb) | 47.4% | 4.52+/-4.09 | Medium | Successful All |
| 34 | FPPS | 2F94 (pdb) | Farnesyl diphosphate synthase | 30 | 2F94 (pdb) | 15.4% | 2.69+/-0.8 | Very Hard | Successful All |
| 35 | PGH2 | 3HS7 (pdb) | Cyclooxygenase-2 | 30 | 4OTY (pdb) | 31.6% | 4.67+/-2.97 | Hard | Successful All |
| 36 | MMP13 | 3KEJ (pdb) | Matrix metalloproteinase 13 | 28 | 3TVC (pdb) | 36.4% | 8.98+/-6.66 | Medium | Successful All |
| 37 | FKB1A | 1FKB (pdb) | FK506-binding protein 1A | 26 | 1BL4 (pdb) | 70.6% | 2.99+/-3.55 | Medium | Successful All |
| 38 | PDE5A | 1UHO (pdb) | Phosphodiesterase 5A | 26 | 3B2R (pdb) | 25.0% | 4.43+/-2.39 | Hard | Successful All |
| 39 | VGFR2 | 3CPB (pdb) | Vascular endothelial growth factor receptor 2 | 24 | 2RL5 (pdb) | 65.0% | 4.72+/-5.21 | Medium | Successful All |
| 40 | HXK4 | 1V4S (pdb) | Hexokinase type IV | 24 | 1V4S (pdb) | 46.2% | 3.87+/-2.84 | Medium | Successful All |
| 41 | GRIK1 | 4DLD (pdb) | Glutamate receptor ionotropic kainate 1 | 23 | 3FVN (pdb) | 54.5% | 3.25+/-2.19 | Medium | Successful All |
| 42 | FNTA | 1KZO (pdb) | Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit | 23 | 1QBQ (pdb) | 14.3% | 6.48+/-3.19 | Very Hard | Successful All |
| 43 | FABP4 | 1G74 (pdb) | Fatty acid binding protein adipocyte | 22 | 1G74 (pdb) | 20.0% | 4.23+/-1.9 | Very Hard | Successful All |
| 44 | XIAP | 3HL5 (pdb) | Inhibitor of apoptosis protein 3 | 21 | 3HL5 (pdb) | 80.0% | 1.5+/-1.02 | Easy | Successful All |
| 45 | FAK1 | 4I4E (pdb) | Focal adhesion kinase 1 | 21 | 3BZ3 (pdb) | 35.3% | 6.6+/-5.25 | Medium | Successful All |
| 46 | CASP3 | 1GFW (pdb) | Caspase-3 | 21 | 2CNK (pdb) | 0.0% | 6.34+/-1.68 | Very Hard | Successful All |
| 47 | PPARD | 2J14 (pdb) | Peroxisome proliferator-activated receptor delta | 21 | 3D5F (pdb) | 58.3% | 3.77+/-3.24 | Medium | Successful All |
| 48 | HMDH | 1HWJ (pdb) | HMG-CoA reductase | 19 | 3CCT (pdb) | 94.4% | 1.11+/-0.61 | Easy | Successful All |
| 49 | PGH1 | 1IGX (pdb) | Cyclooxygenase-1 | 19 | 3KK6 (pdb) | 60.0% | 3.49+/-3.37 | Medium | Successful All |
| 50 | MCR | 3VHV (pdb) | Mineralocorticoid receptor | 18 | 3WFF (pdb) | 100.0% | 0.52+/-0.27 | Easy | Successful All |
| 51 | PRGR | 1A28 (pdb) | Progesterone receptor | 18 | 2W8Y (pdb) | 76.9% | 1.79+/-1.93 | Easy | Successful All |
| 52 | PYGM | 1C8K (pdb) | Muscle glycogen phosphorylase | 18 | 1C8K (pdb) | 21.4% | 5.43+/-4.22 | Very Hard | Successful All |
| 53 | GCR | 3K23 (pdb) | Glucocorticoid receptor | 17 | 3K23 (pdb) | 90.9% | 1.74+/-1.43 | Easy | Successful All |
| 54 | PARP1 | 2RD6 (pdb) | Poly [ADP-ribose] polymerase-1 | 17 | 2RD6 (pdb) | 66.7% | 3.2+/-3.04 | Medium | Successful All |
| 55 | ADRB1 | 2Y02 (pdb) | Beta-1 adrenergic receptor | 15 | 3ZPQ (pdb) | 66.7% | 2.64+/-2.73 | Medium | Successful All |
| 56 | ADA | 1NDZ (pdb) | Adenosine deaminase | 15 | 2Z7G (pdb) | 53.8% | 3.81+/-2.96 | Medium | Successful All |
| 57 | PPARA | 1K7L (pdb) | Peroxisome proliferator-activated receptor alpha | 15 | 1K7L (pdb) | 50.0% | 4.14+/-3.65 | Medium | Successful All |
| 58 | TGFR1 | 2X7O (pdb) | TGF-beta receptor type I | 15 | 2X7O (pdb) | 45.5% | 3.48+/-2.53 | Medium | Successful All |
| 59 | THB | 1R6G (pdb) | Thyroid hormone receptor beta-1 | 14 | 1Q4X (pdb) | 100.0% | 0.95+/-0.37 | Easy | Successful All |
| 60 | UROK | 1U6Q (pdb) | Urokinase-type plasminogen activator | 14 | 2R2W (pdb) | 45.5% | 2.92+/-2.1 | Medium | Successful All |
| 61 | MAPK2 | 2PZY (pdb) | MAP kinase-activated protein kinase 2 | 13 | 3M2W (pdb) | 63.6% | 2.65+/-1.92 | Medium | Successful All |
| 62 | IGF1R | 3I81 (pdb) | Insulin-like growth factor I receptor | 13 | 3I81 (pdb) | 27.3% | 5.48+/-3.38 | Hard | Successful All |
| 63 | ITAL | 2ICA (pdb) | Leukocyte adhesion glycoprotein LFA-1 alpha | 13 | 2O7N (pdb) | 25.0% | 4.51+/-2.4 | Hard | Successful All |
| 64 | TRYB1 | 2ZA5 (pdb) | Tryptase beta-1 | 13 | 2ZEC (pdb) | 42.9% | 6.96+/-6.58 | Medium | Successful All |
| 65 | NRAM | 1B9T (pdb) | Neuraminidase | 12 | 1B9T (pdb) | 57.1% | 2.73+/-2.11 | Medium | Successful All |
| 66 | CSF1R | 2I0Y (pdb) | Macrophage colony stimulating factor receptor | 12 | 3BEA (pdb) | 50.0% | 4.56+/-3.82 | Medium | Successful All |
| 67 | ROCK1 | 3NCZ (pdb) | Rho-associated protein kinase 1 | 12 | 3TWJ (pdb) | 50.0% | 4.21+/-3.3 | Medium | Successful All |
| 68 | ADA17 | 3LEA (pdb) | ADAM17 | 12 | 3LGP (pdb) | 45.5% | 4.69+/-3.86 | Medium | Successful All |
| 69 | AKT1 | 3CQW (pdb) | Serine/threonine-protein kinase AKT | 11 | 3OW4 (pdb) | 50.0% | 3.25+/-2.43 | Medium | Successful All |
| 70 | TYSY | 1F4F (pdb) | Thymidylate synthase | 11 | 1BID (pdb) | 16.7% | 5.48+/-3.11 | Very Hard | Successful All |
| 71 | DYR | 1DRF (pdb) | Dihydrofolate reductase | 11 | 3NXO (pdb) | 18.2% | 4.61+/-2.42 | Very Hard | Successful All |
| 72 | PLK1 | 2RKU (pdb) | Serine/threonine-protein kinase PLK1 | 10 | 4J52 (pdb) | 50.0% | 3.46+/-3.09 | Medium | Successful All |
| 73 | DEF | 1BSK (pdb) | Peptide deformylase | 10 | 1BSK (pdb) | 75.0% | 1.99+/-1.77 | Easy | Successful All |
| 74 | AKT2 | 1O6K (pdb) | Serine/threonine-protein kinase AKT2 | 10 | 3E8D (pdb) | 37.5% | 4.53+/-3.04 | Medium | Successful All |
| 75 | ADRB2 | 2RH1 (pdb) | Beta-2 adrenergic receptor | 9 | 3D4S (pdb) | 80.0% | 1.43+/-0.58 | Easy | Successful All |
| 76 | GLCM | 2WCG (pdb) | Beta-glucocerebrosidase | 9 | 2XWE (pdb) | 71.4% | 1.52+/-1.19 | Medium | Successful All |
| 77 | PUR2 | 1NJS (pdb) | GAR transformylase | 9 | 1NJS (pdb) | 50.0% | 2.94+/-2.92 | Medium | Successful All |
| 78 | WEE1 | 1X8B (pdb) | Serine/threonine-protein kinase WEE1 | 8 | 3BI6 (pdb) | 100.0% | 0.75+/-0.5 | Easy | Successful All |
| 79 | PA2GA | 1DB4 (pdb) | Phospholipase A2 group IIA | 8 | 1DB5 (pdb) | 80.0% | 2.21+/-2.69 | Easy | Successful All |
| 80 | HIVIN | 3NF7 (pdb) | Human immunodeficiency virus type 1 integrase | 8 | 3NF8 (pdb) | 75.0% | 2.67+/-2.78 | Medium | Successful All |
| 81 | ACE | 2OC2 (pdb) | Angiotensin-converting enzyme | 8 | 2OC2 (pdb) | 50.0% | 3.92+/-2.79 | Medium | Successful All |
| 82 | MP2K1 | 3EQF (pdb) | Dual specificity mitogen-activated protein kinase kinase 1 | 8 | 3ZM4 (pdb) | 28.6% | 5.64+/-4.77 | Hard | Successful All |
| 83 | HDAC8 | 3SFF (pdb) | Histone deacetylase 8 | 7 | 3SFF (pdb) | 50.0% | 4.12+/-3.66 | Medium | Successful All |
| 84 | CP3A4 | 3NXU (pdb) | Cytochrome P450 3A4 | 7 | 3NXU (pdb) | 0.0% | Very Hard | Successful All | |
| 85 | KIT | 3G0E (pdb) | Stem cell growth factor receptor | 6 | 3G0F (pdb) | 40.0% | 6.71+/-5.3 | Medium | Successful All |
| 86 | PNPH | 3BGS (pdb) | Purine nucleoside phosphorylase | 6 | 2ON6 (pdb) | 60.0% | 2.73+/-2.38 | Medium | Successful All |
| 87 | CXCR4 | 3ODU (pdb) | C-X-C chemokine receptor type 4 | 4 | 3OE8 (pdb) | 0.0% | 5.37+/-0.41 | Very Hard | Successful All |
| 88 | PYRD | 1D3G (pdb) | Dihydroorotate dehydrogenase | 4 | 1D3G (pdb) | 25.0% | 5.29+/-3.93 | Very Hard | Successful All |
| 89 | SAHH | 1LI4 (pdb) | Adenosylhomocysteinase | 3 | 1LI4 (pdb) | 100.0% | 0.24+/-0.00 | Easy | Successful All |
| 90 | HDAC2 | 3MAX (pdb) | Histone deacetylase 2 | 3 | 4LY1 (pdb) | 66.7% | 3.41+/-3.96 | Medium | Successful All |
| 91 | CP2C9 | 1R9O (pdb) | Cytochrome P450 2C9 | 3 | 1R9O (pdb) | 22.2% | 5.41+/-2.63 | Very Hard | Successful All |
| 92 | AOFB | 1S3B (pdb) | Monoamine oxidase B | 3 | 1S3B (pdb) | 22.2% | 3.53+/-1.61 | Very Hard | Successful All |
| 93 | ALDR | 2HV5 (pdb) | Aldose reductase | 3 | 2HV5 (pdb) | 0.0% | Very Hard | Successful All | |
| 94 | KITH | 2B8T (pdb) | Thymidine kinase | 2 | 2UZ3 (pdb) | 100.0% | 0.98+/-0.45 | Easy | Successful All |
| 95 | AA2AR | 3EML (pdb) | Adenosine A2a receptor | 2 | 3QAK (pdb) | 0.0% | 10.24+/-1.76 | 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 © 2024 Shayne Wierbowski - University of Scranton. Website content © 2024 Jim Zheng - University of Pittsburgh. All rights reserved.