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
39.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.55
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (12/22 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 (-1.001 kcal/mol/HA)
✓ Good fit quality (FQ -9.75)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (39.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-31.019
kcal/mol
LE
-1.001
kcal/mol/HA
Fit Quality
-9.75
FQ (Leeson)
HAC
31
heavy atoms
MW
457
Da
LogP
3.84
cLogP
Interaction summary
HB 10
HY 9
PI 1
CLASH 5
⚠ Exposure 54%
Interaction summary
HB 10
HY 9
PI 1
CLASH 5
⚠ Exposure 54%
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
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 10
Exposed 12
LogP 3.84
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.375 | Score | -31.019 |
|---|---|---|---|
| Inter norm | -1.066 | Intra norm | 0.066 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 10 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; high strain Δ 39.1 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 8 | Strict recall | 0.53 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 591 | 1.448398973137486 | -0.960184 | -28.9048 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 581 | 1.9786488300597957 | -0.865659 | -28.5707 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 596 | 2.8828698978375003 | -0.625605 | -19.8303 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 604 | 3.3008265012864664 | -0.727321 | -22.6133 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 4.375178238702462 | -1.0662 | -31.019 | 10 | 22 | 19 | 0.90 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.019kcal/mol
Ligand efficiency (LE)
-1.0006kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.748
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
456.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.84
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-28.35kcal/mol
Minimised FF energy
-67.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
705.0Ų
Total solvent-accessible surface area of free ligand
BSA total
623.6Ų
Buried surface area upon binding
BSA apolar
494.0Ų
Hydrophobic contacts buried
BSA polar
129.6Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1433.3Ų
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
493.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)