Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
13.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.52, Jaccard 0.37, H-bond role recall 0.36
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.300 kcal/mol/HA)
✓ Good fit quality (FQ -12.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (13.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-35.089
kcal/mol
LE
-1.300
kcal/mol/HA
Fit Quality
-12.12
FQ (Leeson)
HAC
27
heavy atoms
MW
377
Da
LogP
3.39
cLogP
Interaction summary
HB 6
HY 6
PI 0
CLASH 6
⚠ Exposure 40%
Interaction summary
HB 6
HY 6
PI 0
CLASH 6
⚠ Exposure 40%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 12
Exposed 8
LogP 3.39
H-bonds 6
Exposed fragments:
phenyl (2/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 2.898 | Score | -35.089 |
|---|---|---|---|
| Inter norm | -1.282 | Intra norm | -0.018 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash | ||
| Residues |
ALA24
ALA70
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU31
LEU39
LYS127
LYS26
SER22
SER27
SER28
THR44
THR69
| ||
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 | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 378 | 0.45254100967401695 | -1.19369 | -33.2631 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 0.5753386101624237 | -0.979431 | -23.4038 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 445 | 0.9634963465238795 | -0.972905 | -25.4432 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 1.9316215269590413 | -0.873952 | -22.2228 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 359 | 2.8977259071513566 | -1.28181 | -35.089 | 6 | 20 | 11 | 0.52 | 0.36 | - | no | Current |
| 461 | 3.049567594159186 | -0.847236 | -21.5065 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 3.266816838999127 | -0.920746 | -22.9429 | 10 | 11 | 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
-35.089kcal/mol
Ligand efficiency (LE)
-1.2996kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.125
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
377.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.39
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.06kcal/mol
Minimised FF energy
72.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
587.8Ų
Total solvent-accessible surface area of free ligand
BSA total
545.7Ų
Buried surface area upon binding
BSA apolar
453.9Ų
Hydrophobic contacts buried
BSA polar
91.8Ų
Polar contacts buried
Fraction buried
92.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1359.3Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
498.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)