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
31.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.18
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (16/28 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 (-0.755 kcal/mol/HA)
✓ Good fit quality (FQ -7.42)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Very high strain energy (31.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-24.153
kcal/mol
LE
-0.755
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
32
heavy atoms
MW
435
Da
LogP
1.84
cLogP
Interaction summary
HB 6
HY 6
PI 1
CLASH 5
⚠ Exposure 57%
Interaction summary
HB 6
HY 6
PI 1
CLASH 5
⚠ Exposure 57%
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
57% of hydrophobic surface appears solvent-exposed (16/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 12
Exposed 16
LogP 1.84
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.690 | Score | -24.153 |
|---|---|---|---|
| Inter norm | -0.958 | Intra norm | 0.204 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 6 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 31.9 | ||
| Residues |
ALA158
ALA24
ALA70
ASN126
ASN41
ASP68
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU39
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 3 | Strict recall | 0.20 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| HB same residue | 2 | HB residue recall | 0.18 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 152 | 3.689835022759314 | -0.958348 | -24.1532 | 6 | 22 | 17 | 0.81 | 0.18 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.153kcal/mol
Ligand efficiency (LE)
-0.7548kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.423
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
434.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.84
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
167.27kcal/mol
Minimised FF energy
135.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
731.6Ų
Total solvent-accessible surface area of free ligand
BSA total
634.5Ų
Buried surface area upon binding
BSA apolar
592.8Ų
Hydrophobic contacts buried
BSA polar
41.8Ų
Polar contacts buried
Fraction buried
86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1567.1Ų
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
491.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)