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