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 strong
SASA done
Strain ΔE
16.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.82, H-bond role recall 0.30
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (9/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.037 kcal/mol/HA)
✓ Good fit quality (FQ -9.67)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-27.998
kcal/mol
LE
-1.037
kcal/mol/HA
Fit Quality
-9.67
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
3.67
cLogP
Final rank
2.7452
rank score
Inter norm
-1.010
normalised
Contacts
15
H-bonds 6
Interaction summary
HBA 6
HY 4
PI 3
CLASH 2
Interaction summary
HBA 6
HY 4
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 14 | Native recall | 0.88 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 3 | HB residue recall | 0.30 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 102 | 1.517836335498182 | -1.03041 | -28.7494 | 6 | 15 | 14 | 0.88 | 0.30 | - | no | Open |
| 107 | 2.622610430889731 | -1.11591 | -28.2968 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 353 | 2.7452201618408285 | -1.0098 | -27.9976 | 6 | 15 | 14 | 0.88 | 0.30 | - | no | Current |
| 334 | 3.6216855532747294 | -0.93662 | -19.8682 | 14 | 14 | 5 | 0.31 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.998kcal/mol
Ligand efficiency (LE)
-1.0369kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.674
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.67
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.16kcal/mol
Minimised FF energy
1.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
647.5Ų
Total solvent-accessible surface area of free ligand
BSA total
471.6Ų
Buried surface area upon binding
BSA apolar
336.0Ų
Hydrophobic contacts buried
BSA polar
135.6Ų
Polar contacts buried
Fraction buried
72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2144.4Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
770.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)