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py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: weak
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 0
π–π 0
Clashes 7
Severe clashes 0
⚠ Hydrophobic exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (17/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 0
Exposed 17
LogP 2.9
H-bonds 6
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.9719247438229197 | Score | -23.9807 |
|---|---|---|---|
| Inter norm | -0.813555 | Intra norm | -0.145671 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 6 |
| Artifact reason | geometry warning; 5 clashes; 7 protein contact clashes; high strain Δ 32.6 | ||
| Residues | A:ARG242;A:ARG337;A:ASP243;A:ASP385;A:GLU384;A:LEU339;A:PHE383;A:SER282;A:THR241;A:VAL336 | ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 7 |
| IFP residues | A:ARG22; A:ARG242; A:ARG337; A:ARG342; A:ASP243; A:ASP385; A:GLN341; A:GLU384; A:LEU25; A:LEU339; A:LEU382; A:PRO340; A:PRO344; A:SER282; A:THR241 | ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.47 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
Hydrophobic contacts
No hydrophobic contacts detected for this pose.
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1956 | 3.9719247438229197 | -0.813555 | -23.9807 | 6 | 10 | 8 | 0.53 | 0.60 | - | no | Current |
| 1631 | 3.990097491650414 | -1.20845 | -31.8412 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1948 | 4.077178934207164 | -0.994198 | -21.1376 | 8 | 11 | 8 | 0.53 | 0.20 | - | no | Open |
| 1953 | 4.394101442736083 | -0.656907 | -15.8199 | 7 | 12 | 8 | 0.53 | 0.60 | - | no | Open |
| 1950 | 4.520508479762334 | -0.590778 | -18.3536 | 8 | 12 | 6 | 0.40 | 0.40 | - | no | Open |
| 1963 | 4.610602508560925 | -0.931318 | -17.1628 | 7 | 12 | 8 | 0.53 | 0.20 | - | no | Open |
| 1954 | 4.637730843772612 | -0.663104 | -16.5608 | 8 | 8 | 5 | 0.33 | 0.20 | - | no | Open |
| 1633 | 4.953641725635689 | -0.97132 | -23.3679 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1947 | 5.145783295154316 | -1.01905 | -17.88 | 9 | 13 | 8 | 0.53 | 0.20 | - | no | Open |
| 1622 | 5.629112617554057 | -1.08014 | -18.9447 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1625 | 5.695197473665788 | -1.06651 | -27.3037 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1623 | 4.722887485101648 | -1.15029 | -25.7821 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1961 | 4.986613216964748 | -0.868934 | -22.2924 | 8 | 12 | 8 | 0.53 | 0.40 | - | yes | Open |
| 1627 | 5.0231157270417395 | -1.0603 | -27.5693 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1629 | 5.100339596450561 | -1.13847 | -29.6603 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1964 | 5.586540570182502 | -0.831982 | -25.4771 | 7 | 10 | 8 | 0.53 | 0.20 | - | yes | Open |
| 1952 | 5.720935992138321 | -1.00761 | -24.422 | 6 | 10 | 8 | 0.53 | 0.20 | - | yes | Open |
| 1958 | 5.93947971692062 | -0.757363 | -19.2059 | 6 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 1966 | 6.174429901740043 | -0.491133 | -9.00137 | 6 | 9 | 6 | 0.40 | 0.40 | - | yes | Open |
| 1960 | 6.459949314204331 | -0.944202 | -26.3266 | 8 | 11 | 8 | 0.53 | 0.40 | - | yes | Open |
| 1619 | 6.629146215182119 | -1.2819 | -34.2305 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1959 | 6.830981333984871 | -1.04153 | -22.8326 | 9 | 12 | 8 | 0.53 | 0.60 | - | yes | Open |
| 1632 | 7.055319422142833 | -1.20582 | -30.1724 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1620 | 7.066023679251342 | -1.18159 | -28.5847 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1955 | 7.989508370292556 | -0.828912 | -16.9316 | 7 | 12 | 8 | 0.53 | 0.60 | - | yes | Open |
| 1626 | 8.08260769643385 | -0.888001 | -24.1729 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1618 | 10.000134041616684 | -1.14276 | -21.649 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1951 | 55.443076384166346 | -0.993738 | -21.8316 | 7 | 11 | 9 | 0.60 | 0.40 | - | yes | Open |
| 1949 | 57.1922033686288 | -0.657676 | -12.3713 | 5 | 10 | 7 | 0.47 | 0.40 | - | yes | Open |
| 1962 | 57.39265247614407 | -0.90039 | -26.2021 | 10 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 1624 | 57.393071639128145 | -1.19785 | -27.8302 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1628 | 58.94178901634015 | -0.950145 | -24.4336 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1957 | 59.53003160587106 | -0.595371 | -15.7347 | 8 | 9 | 7 | 0.47 | 0.40 | - | yes | Open |
| 1630 | 59.61896838299392 | -1.09222 | -16.5992 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1965 | 61.035180875951205 | -0.69079 | -13.6559 | 7 | 8 | 6 | 0.40 | 0.40 | - | yes | Open |
| 1621 | 62.205471001928714 | -1.10376 | -30.0534 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.