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 strong
SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.27
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (13/23 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 (-0.919 kcal/mol/HA)
✓ Good fit quality (FQ -8.57)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-24.812
kcal/mol
LE
-0.919
kcal/mol/HA
Fit Quality
-8.57
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
5.41
cLogP
Interaction summary
HB 10
HY 10
PI 1
CLASH 7
⚠ Exposure 56%
Interaction summary
HB 10
HY 10
PI 1
CLASH 7
⚠ Exposure 56%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (13/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 10
Exposed 13
LogP 5.41
H-bonds 10
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.349 | Score | -24.812 |
|---|---|---|---|
| Inter norm | -1.123 | Intra norm | 0.204 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU73
GLY23
GLY25
GLY71
LYS127
LYS159
LYS26
PHE38
SER27
SER28
THR44
THR69
| ||
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 | ||
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 322 | 0.8278075936041438 | -1.32071 | -32.9059 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 356 | 0.9693317372851367 | -0.896093 | -18.51 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 3.6612808815022593 | -0.956451 | -23.6271 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 348 | 4.023415965506665 | -0.910424 | -13.4768 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 4.349104779598979 | -1.12272 | -24.8121 | 10 | 18 | 13 | 0.62 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.812kcal/mol
Ligand efficiency (LE)
-0.9190kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.574
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.41
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.67kcal/mol
Minimised FF energy
66.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
641.2Ų
Total solvent-accessible surface area of free ligand
BSA total
512.0Ų
Buried surface area upon binding
BSA apolar
429.4Ų
Hydrophobic contacts buried
BSA polar
82.6Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1376.3Ų
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
543.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)