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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
44.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.45
Reason: strain 44.7 kcal/mol
strain ΔE 44.7 kcal/mol
1 protein-contact clashes
70% of hydrophobic surface is solvent-exposed (16/23 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. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 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 Risk
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.744 kcal/mol/HA)
✓ Good fit quality (FQ -7.17)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Extreme strain energy (44.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-22.310
kcal/mol
LE
-0.744
kcal/mol/HA
Fit Quality
-7.17
FQ (Leeson)
HAC
30
heavy atoms
MW
418
Da
LogP
4.07
cLogP
Final rank
4.1101
rank score
Inter norm
-0.917
normalised
Contacts
17
H-bonds 8
Interaction summary
HBA 8
HY 2
PI 1
CLASH 1
Interaction summary
HBA 8
HY 2
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.76 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 489 | 2.636037679981359 | -0.764182 | -22.927 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 386 | 4.110089435729965 | -0.916695 | -22.3096 | 8 | 17 | 13 | 0.76 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.310kcal/mol
Ligand efficiency (LE)
-0.7437kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.174
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.07
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
44.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.52kcal/mol
Minimised FF energy
58.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.0Ų
Total solvent-accessible surface area of free ligand
BSA total
476.5Ų
Buried surface area upon binding
BSA apolar
395.3Ų
Hydrophobic contacts buried
BSA polar
81.2Ų
Polar contacts buried
Fraction buried
69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2281.1Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
706.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)