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
9.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.55
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (11/11 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
GDS: UNSAFE
UL GreenDrugScore ML model
ECOscore
0.352
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.550
ADMET + ECO + DL
ADMETscore (GDS)
0.680
absorption · distr. · metab.
DLscore
0.441
drug-likeness
P(SAFE)
0.31
GDS classification
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.596 kcal/mol/HA)
✓ Good fit quality (FQ -13.08)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (9.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.327
kcal/mol
LE
-1.596
kcal/mol/HA
Fit Quality
-13.08
FQ (Leeson)
HAC
19
heavy atoms
MW
282
Da
LogP
-0.16
cLogP
Final rank
3.8953
rank score
Inter norm
-1.620
normalised
Contacts
17
H-bonds 11
Interaction summary
HBD 1
HBA 7
HY 0
PI 0
CLASH 3
Interaction summary
HBD 1
HBA 7
HY 0
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 311 | 3.8952903470879194 | -1.61952 | -30.3267 | 11 | 17 | 12 | 0.57 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.327kcal/mol
Ligand efficiency (LE)
-1.5961kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.083
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
282.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.16
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-72.04kcal/mol
Minimised FF energy
-81.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
460.1Ų
Total solvent-accessible surface area of free ligand
BSA total
423.6Ų
Buried surface area upon binding
BSA apolar
265.9Ų
Hydrophobic contacts buried
BSA polar
157.7Ų
Polar contacts buried
Fraction buried
92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1160.2Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
503.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)