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
22.9 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.57, Jaccard 0.43, H-bond role recall 0.36
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (7/19 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 (-1.072 kcal/mol/HA)
✓ Good fit quality (FQ -10.00)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-28.939
kcal/mol
LE
-1.072
kcal/mol/HA
Fit Quality
-10.00
FQ (Leeson)
HAC
27
heavy atoms
MW
417
Da
LogP
4.51
cLogP
Interaction summary
HB 10
HY 4
PI 0
CLASH 9
⚠ Exposure 36%
Interaction summary
HB 10
HY 4
PI 0
CLASH 9
⚠ Exposure 36%
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
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 12
Exposed 7
LogP 4.51
H-bonds 10
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.999 | Score | -28.939 |
|---|---|---|---|
| Inter norm | -1.222 | Intra norm | 0.150 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 10 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 22.9 | ||
| Residues |
ALA24
ALA70
ASN41
ASP68
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.43 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 597 | 0.6640614952139893 | -0.977124 | -27.6842 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 580 | 0.9038309412884264 | -0.905331 | -23.8593 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 587 | 1.884441831644803 | -1.32864 | -37.842 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 612 | 2.292126539421007 | -0.903342 | -25.3788 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 2.355909460894976 | -0.876448 | -21.989 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 607 | 3.9993046300034925 | -1.22165 | -28.9394 | 10 | 19 | 12 | 0.57 | 0.36 | - | no | Current |
| 598 | 5.264689604629017 | -1.03745 | -28.3885 | 10 | 19 | 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
-28.939kcal/mol
Ligand efficiency (LE)
-1.0718kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.000
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
416.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.51
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
10.02kcal/mol
Minimised FF energy
-12.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
617.7Ų
Total solvent-accessible surface area of free ligand
BSA total
507.6Ų
Buried surface area upon binding
BSA apolar
384.5Ų
Hydrophobic contacts buried
BSA polar
123.2Ų
Polar contacts buried
Fraction buried
82.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1320.3Ų
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
530.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)