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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
22.4 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.00
Reason: 10 internal clashes
10 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (13/21 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 Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.863 kcal/mol/HA)
✓ Good fit quality (FQ -8.33)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-25.896
kcal/mol
LE
-0.863
kcal/mol/HA
Fit Quality
-8.33
FQ (Leeson)
HAC
30
heavy atoms
MW
426
Da
LogP
3.82
cLogP
Final rank
0.5773
rank score
Inter norm
-0.863
normalised
Contacts
20
H-bonds 3
Interaction summary
HBA 1
HY 6
PI 1
CLASH 0
Interaction summary
HBA 1
HY 6
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.64 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 596 | 0.5773062689630676 | -0.862611 | -25.896 | 3 | 20 | 16 | 0.76 | 0.00 | - | no | Current |
| 591 | 1.036432703761499 | -0.853836 | -24.2863 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 605 | 2.0302417119039733 | -0.854506 | -24.5526 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 2.689759316825253 | -0.827482 | -20.2121 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 607 | 4.895650481240657 | -0.715065 | -17.8757 | 7 | 12 | 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
-25.896kcal/mol
Ligand efficiency (LE)
-0.8632kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
426.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.82
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-42.16kcal/mol
Minimised FF energy
-64.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
696.0Ų
Total solvent-accessible surface area of free ligand
BSA total
552.6Ų
Buried surface area upon binding
BSA apolar
449.2Ų
Hydrophobic contacts buried
BSA polar
103.5Ų
Polar contacts buried
Fraction buried
79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1604.3Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
628.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)