Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
63% of hydrophobic surface is solvent-exposed (12/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.958 kcal/mol/HA)
✓ Good fit quality (FQ -8.94)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (16.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.871
kcal/mol
LE
-0.958
kcal/mol/HA
Fit Quality
-8.94
FQ (Leeson)
HAC
27
heavy atoms
MW
387
Da
LogP
3.51
cLogP
Final rank
3.3449
rank score
Inter norm
-0.965
normalised
Contacts
13
H-bonds 8
Interaction summary
HBD 2
HBA 4
HY 2
PI 0
CLASH 1
Interaction summary
HBD 2
HBA 4
HY 2
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:ORX602
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 84 | 0.8978347699667351 | -0.856296 | -18.6325 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 148 | 1.357888497962855 | -1.1807 | -25.8924 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 1.7243640298374872 | -0.868266 | -19.382 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 1.7561042414858175 | -0.860322 | -19.3331 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 172 | 2.1483737556840357 | -0.787852 | -18.4121 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 179 | 3.3422147983594046 | -0.973711 | -26.1073 | 7 | 13 | 8 | 0.53 | 0.40 | - | no | Open |
| 123 | 3.34487200823826 | -0.964684 | -25.8709 | 8 | 13 | 8 | 0.53 | 0.40 | - | no | Current |
| 14 | 3.421092231944404 | -0.988207 | -26.0904 | 7 | 14 | 8 | 0.53 | 0.40 | - | no | Open |
| 68 | 3.5108182235106415 | -0.943196 | -24.5073 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 126 | 3.999031944814804 | -1.11537 | -28.1146 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 4.234950268980408 | -0.850058 | -20.7434 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 162 | 51.82397871238766 | -0.869886 | -18.9182 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 119 | 53.49803393991051 | -0.976064 | -25.9699 | 7 | 14 | 8 | 0.53 | 0.40 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.871kcal/mol
Ligand efficiency (LE)
-0.9582kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.939
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
387.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.51
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
26.67kcal/mol
Minimised FF energy
10.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
662.9Ų
Total solvent-accessible surface area of free ligand
BSA total
469.0Ų
Buried surface area upon binding
BSA apolar
393.0Ų
Hydrophobic contacts buried
BSA polar
76.0Ų
Polar contacts buried
Fraction buried
70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2503.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1388.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)