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
20.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.95, Jaccard 0.91, H-bond role recall 0.64
Reason: no major geometry red flags detected
2 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (7/17 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 (-1.234 kcal/mol/HA)
✓ Good fit quality (FQ -11.37)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (20.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-32.092
kcal/mol
LE
-1.234
kcal/mol/HA
Fit Quality
-11.37
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
2.33
cLogP
Interaction summary
HB 10
HY 7
PI 1
CLASH 2
⚠ Exposure 41%
Interaction summary
HB 10
HY 7
PI 1
CLASH 2
⚠ Exposure 41%
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP 2.33
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.504 | Score | -32.092 |
|---|---|---|---|
| Inter norm | -1.264 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 20.3 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
| ||
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.91 | RMSD | - |
| HB strict | 8 | Strict recall | 0.53 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 132 | 0.6034787560662435 | -0.986253 | -17.9228 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 138 | 1.4476132232114785 | -1.32116 | -31.3906 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 1.8348160871656356 | -1.07441 | -21.076 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 3.5037539024917495 | -1.26397 | -32.0923 | 10 | 21 | 20 | 0.95 | 0.64 | - | no | Current |
| 61 | 3.9546360904873596 | -0.94287 | -20.9441 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 123 | 4.331751406084817 | -0.886047 | -18.545 | 6 | 15 | 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
-32.092kcal/mol
Ligand efficiency (LE)
-1.2343kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.372
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-56.73kcal/mol
Minimised FF energy
-77.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
595.3Ų
Total solvent-accessible surface area of free ligand
BSA total
528.6Ų
Buried surface area upon binding
BSA apolar
371.6Ų
Hydrophobic contacts buried
BSA polar
157.1Ų
Polar contacts buried
Fraction buried
88.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1288.7Ų
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
508.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)