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 medium
Native strong
SASA done
Strain ΔE
11.2 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.55, H-bond role recall 0.67
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.137 kcal/mol/HA)
✓ Good fit quality (FQ -10.47)
✓ Good H-bonds (4 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (11.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.552
kcal/mol
LE
-1.137
kcal/mol/HA
Fit Quality
-10.47
FQ (Leeson)
HAC
26
heavy atoms
MW
351
Da
LogP
0.96
cLogP
Final rank
1.7532
rank score
Inter norm
-1.169
normalised
Contacts
14
H-bonds 10
Interaction summary
HBD 3
HBA 1
HY 4
PI 1
CLASH 3
Interaction summary
HBD 3
HBA 1
HY 4
PI 1
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 | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.65 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 4 | HB role recall | 0.67 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 242 | 0.013117550346434954 | -1.27485 | -32.1304 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 0.34940278881708586 | -0.995743 | -23.256 | 4 | 10 | 10 | 0.59 | 0.67 | - | no | Open |
| 235 | 1.7531652320878486 | -1.16928 | -29.5525 | 10 | 14 | 11 | 0.65 | 0.67 | - | no | Current |
| 168 | 2.7555481195899034 | -1.09563 | -21.4154 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 260 | 3.7764900594995785 | -1.04939 | -26.037 | 7 | 14 | 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
-29.552kcal/mol
Ligand efficiency (LE)
-1.1366kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.43kcal/mol
Minimised FF energy
8.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.4Ų
Total solvent-accessible surface area of free ligand
BSA total
540.1Ų
Buried surface area upon binding
BSA apolar
426.2Ų
Hydrophobic contacts buried
BSA polar
113.9Ų
Polar contacts buried
Fraction buried
86.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1623.0Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1047.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)