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 high
Native strong
SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
59% of hydrophobic surface appears solvent-exposed (10/17 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 (-1.188 kcal/mol/HA)
✓ Good fit quality (FQ -10.49)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.327
kcal/mol
LE
-1.188
kcal/mol/HA
Fit Quality
-10.49
FQ (Leeson)
HAC
23
heavy atoms
MW
331
Da
LogP
3.59
cLogP
Interaction summary
HB 8
HY 2
PI 1
CLASH 1
⚠ Exposure 58%
Interaction summary
HB 8
HY 2
PI 1
CLASH 1
⚠ Exposure 58%
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
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 7
Exposed 10
LogP 3.59
H-bonds 8
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.700 | Score | -27.327 |
|---|---|---|---|
| Inter norm | -1.354 | Intra norm | 0.166 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; moderate strain Δ 22.9 | ||
| Residues |
ALA158
ALA24
ASN126
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LYS127
LYS159
LYS26
PHE38
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 96 | -0.12304124545237619 | -1.39622 | -27.7103 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 1.6762107964268975 | -1.20315 | -26.1454 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 2.7001241589986824 | -1.35434 | -27.3266 | 8 | 19 | 14 | 0.67 | 0.27 | - | no | Current |
| 62 | 2.716998234569074 | -1.27524 | -28.6052 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 67 | 3.0786886463102823 | -1.46105 | -30.4188 | 6 | 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
-27.327kcal/mol
Ligand efficiency (LE)
-1.1881kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.486
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.59
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.68kcal/mol
Minimised FF energy
14.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
568.2Ų
Total solvent-accessible surface area of free ligand
BSA total
517.3Ų
Buried surface area upon binding
BSA apolar
382.4Ų
Hydrophobic contacts buried
BSA polar
134.9Ų
Polar contacts buried
Fraction buried
91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1307.4Ų
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
489.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)