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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.45
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (4/10 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 (-1.528 kcal/mol/HA)
✓ Good fit quality (FQ -12.52)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (92% SASA buried)
✗ Very high strain energy (31.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.030
kcal/mol
LE
-1.528
kcal/mol/HA
Fit Quality
-12.52
FQ (Leeson)
HAC
19
heavy atoms
MW
298
Da
LogP
0.82
cLogP
Interaction summary
HB 12
HY 2
PI 0
CLASH 4
⚠ Exposure 40%
Interaction summary
HB 12
HY 2
PI 0
CLASH 4
⚠ 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 (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 10
Buried (contacted) 6
Exposed 4
LogP 0.82
H-bonds 12
Exposed fragments:
phenyl (4/6 atoms exposed)
| Final rank | 5.238 | Score | -29.030 |
|---|---|---|---|
| Inter norm | -1.635 | Intra norm | 0.107 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 12 |
| Artifact reason | geometry warning; 9 clashes; 4 protein clashes; high strain Δ 31.2 | ||
| Residues |
ALA24
ALA70
ASN41
ASP68
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU39
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 274 | 0.004259456452601552 | -1.19998 | -22.0537 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 1.499994412154343 | -1.10284 | -19.4731 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.0693543880229 | -1.44348 | -27.3657 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 2.7894550963165585 | -1.04816 | -18.5277 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 2.970470011926121 | -1.44374 | -27.3571 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 227 | 3.892181034674322 | -1.33338 | -23.5436 | 14 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 259 | 5.237778050113307 | -1.63455 | -29.0298 | 12 | 17 | 12 | 0.57 | 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
-29.030kcal/mol
Ligand efficiency (LE)
-1.5279kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.524
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
298.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.82
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-50.27kcal/mol
Minimised FF energy
-81.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
460.5Ų
Total solvent-accessible surface area of free ligand
BSA total
425.0Ų
Buried surface area upon binding
BSA apolar
245.7Ų
Hydrophobic contacts buried
BSA polar
179.3Ų
Polar contacts buried
Fraction buried
92.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
57.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1135.0Ų
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
503.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)