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
30.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (7/13 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 (-1.114 kcal/mol/HA)
✓ Good fit quality (FQ -9.99)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Very high strain energy (30.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-26.742
kcal/mol
LE
-1.114
kcal/mol/HA
Fit Quality
-9.99
FQ (Leeson)
HAC
24
heavy atoms
MW
390
Da
LogP
0.89
cLogP
Interaction summary
HB 11
HY 5
PI 1
CLASH 3
⚠ Exposure 53%
Interaction summary
HB 11
HY 5
PI 1
CLASH 3
⚠ Exposure 53%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 6
Exposed 7
LogP 0.89
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.735 | Score | -26.742 |
|---|---|---|---|
| Inter norm | -1.421 | Intra norm | 0.307 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 11 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 30.8 | ||
| Residues |
ALA158
ALA24
ASN126
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 593 | 3.7354699627388626 | -1.4208 | -26.7416 | 11 | 21 | 18 | 0.86 | 0.45 | - | no | Current |
| 580 | 4.025960175151159 | -0.986819 | -19.9183 | 14 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 597 | 4.400529884772353 | -0.977976 | -20.7072 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 589 | 4.415742123828827 | -1.00117 | -22.6809 | 7 | 13 | 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
-26.742kcal/mol
Ligand efficiency (LE)
-1.1142kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.986
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
389.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.89
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-149.30kcal/mol
Minimised FF energy
-180.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
593.7Ų
Total solvent-accessible surface area of free ligand
BSA total
545.5Ų
Buried surface area upon binding
BSA apolar
339.0Ų
Hydrophobic contacts buried
BSA polar
206.5Ų
Polar contacts buried
Fraction buried
91.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1235.2Ų
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
504.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)