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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
56.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.45
Reason: strain 56.1 kcal/mol
strain ΔE 56.1 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (16/16 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
0.768
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.543
ADMET + ECO + DL
ADMETscore (GDS)
0.530
absorption · distr. · metab.
DLscore
0.433
drug-likeness
P(SAFE)
0.16
GDS classification
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.327 kcal/mol/HA)
✓ Good fit quality (FQ -11.89)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Extreme strain energy (56.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-31.843
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-11.89
FQ (Leeson)
HAC
24
heavy atoms
MW
465
Da
LogP
0.89
cLogP
Final rank
5.5857
rank score
Inter norm
-1.375
normalised
Contacts
14
H-bonds 12
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3.505680280424295 | -1.34294 | -31.4204 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 5.585675844707634 | -1.37538 | -31.8429 | 12 | 14 | 11 | 0.52 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.843kcal/mol
Ligand efficiency (LE)
-1.3268kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.891
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
465.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
56.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.27kcal/mol
Minimised FF energy
35.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
582.6Ų
Total solvent-accessible surface area of free ligand
BSA total
436.1Ų
Buried surface area upon binding
BSA apolar
300.4Ų
Hydrophobic contacts buried
BSA polar
135.7Ų
Polar contacts buried
Fraction buried
74.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1282.0Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
531.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)