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 mixed
SASA done
Strain ΔE
12.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.36
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (10/10 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
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 (-1.979 kcal/mol/HA)
✓ Good fit quality (FQ -15.06)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (12.4 kcal/mol)
✗ Geometry warnings
Score
-31.667
kcal/mol
LE
-1.979
kcal/mol/HA
Fit Quality
-15.06
FQ (Leeson)
HAC
16
heavy atoms
MW
222
Da
LogP
-0.19
cLogP
Final rank
2.9555
rank score
Inter norm
-2.113
normalised
Contacts
16
H-bonds 13
Interaction summary
HBD 3
HBA 6
HY 0
PI 0
CLASH 3
Interaction summary
HBD 3
HBA 6
HY 0
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 240 | -0.9575213856046881 | -1.92853 | -27.7645 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 1.3353371102338811 | -1.26392 | -19.2163 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 219 | 1.8619677573339846 | -1.71071 | -27.1737 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 2.208227771750752 | -1.42154 | -21.5833 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 217 | 2.539177750072255 | -1.51499 | -21.7052 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 208 | 2.9554619952564956 | -2.11338 | -31.6674 | 13 | 16 | 11 | 0.52 | 0.36 | - | no | Current |
| 164 | 3.5204397139105086 | -1.77214 | -26.8263 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 3.5327696926214855 | -1.50218 | -21.5641 | 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
-31.667kcal/mol
Ligand efficiency (LE)
-1.9792kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.065
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
16HA
Physicochemical properties
Molecular weight
222.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.19
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.68kcal/mol
Minimised FF energy
30.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
434.8Ų
Total solvent-accessible surface area of free ligand
BSA total
392.9Ų
Buried surface area upon binding
BSA apolar
279.3Ų
Hydrophobic contacts buried
BSA polar
113.7Ų
Polar contacts buried
Fraction buried
90.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1178.6Ų
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
509.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)