Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
35.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.79, H-bond role recall 0.36
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
74% of hydrophobic surface is solvent-exposed (17/23 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 High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.482 kcal/mol/HA)
✓ Good fit quality (FQ -4.78)
✓ Good H-bonds (4 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (35.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-15.899
kcal/mol
LE
-0.482
kcal/mol/HA
Fit Quality
-4.78
FQ (Leeson)
HAC
33
heavy atoms
MW
486
Da
LogP
4.13
cLogP
Final rank
3.7845
rank score
Inter norm
-0.750
normalised
Contacts
17
H-bonds 7
Interaction summary
HBA 4
HY 2
PI 2
CLASH 3
Interaction summary
HBA 4
HY 2
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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 | 15 | Native recall | 0.88 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 484 | 1.6830606252738989 | -0.743187 | -19.2115 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 1.9789215848404698 | -0.917724 | -24.5812 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 2.5136273279812995 | -0.919656 | -24.9115 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 110 | 2.8793248649702754 | -0.805397 | -25.4557 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 126 | 2.9672521965662164 | -0.835595 | -16.7586 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 3.304468521208352 | -0.813519 | -25.9782 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 3.503518404096005 | -1.01121 | -27.3035 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 3.7845323780093345 | -0.749603 | -15.8986 | 7 | 17 | 15 | 0.88 | 0.36 | - | no | Current |
| 484 | 4.235486935676271 | -1.01852 | -28.93 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.899kcal/mol
Ligand efficiency (LE)
-0.4818kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.780
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.64kcal/mol
Minimised FF energy
34.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
777.1Ų
Total solvent-accessible surface area of free ligand
BSA total
524.0Ų
Buried surface area upon binding
BSA apolar
423.1Ų
Hydrophobic contacts buried
BSA polar
100.9Ų
Polar contacts buried
Fraction buried
67.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2334.9Ų
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
678.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)